Query         gi|254780879|ref|YP_003065292.1| hypothetical protein CLIBASIA_03880 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 652
No_of_seqs    232 out of 1214
Neff          7.1 
Searched_HMMs 39220
Date          Mon May 30 00:49:41 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780879.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11649 hypothetical protein; 100.0       0       0  670.2  35.6  344  273-639    71-416 (418)
  2 COG0739 NlpD Membrane proteins 100.0 1.4E-45       0  339.6  19.0  141  473-616   121-267 (277)
  3 PRK10871 nlpD lipoprotein NlpD 100.0 1.5E-43       0  325.3  19.2  119  485-615   254-373 (374)
  4 PRK11637 hypothetical protein; 100.0   2E-44       0  331.5  12.0  121  483-610   280-400 (404)
  5 pfam01551 Peptidase_M23 Peptid 100.0 2.8E-30   7E-35  231.9   9.7   96  511-608     1-96  (96)
  6 COG4942 Membrane-bound metallo  99.9 2.5E-27 6.5E-32  211.1   6.2  128  476-610   289-416 (420)
  7 PRK06148 hypothetical protein;  99.5 1.2E-13   3E-18  114.9   8.4  102  510-611   440-553 (1015)
  8 PRK06149 hypothetical protein;  98.9 2.8E-09 7.2E-14   84.1   6.8   80  510-603   429-508 (972)
  9 pfam04225 OapA Opacity-associa  98.6 6.9E-07 1.8E-11   67.3  10.5   82  276-361     2-83  (85)
 10 PRK10783 mltD membrane-bound l  98.1 5.9E-05 1.5E-09   53.7  10.8  108  273-431   340-447 (449)
 11 COG3061 OapA Cell envelope opa  98.0 0.00017 4.4E-09   50.5  11.6   83  275-361   158-240 (242)
 12 PRK10783 mltD membrane-bound l  97.8 0.00011 2.8E-09   51.8   7.0  122  277-429   264-387 (449)
 13 cd00118 LysM Lysin domain, fou  97.6 9.8E-05 2.5E-09   52.2   4.7   45  278-326     2-46  (46)
 14 smart00257 LysM Lysin motif.    97.5 0.00012   3E-09   51.6   4.3   44  278-325     1-44  (44)
 15 PRK13914 invasion associated s  97.3 0.00055 1.4E-08   46.9   5.1   43  278-325    27-69  (475)
 16 pfam01476 LysM LysM domain. Th  97.2 0.00041   1E-08   47.8   4.2   43  279-326     1-43  (43)
 17 PRK06347 autolysin; Reviewed    97.0  0.0011 2.9E-08   44.7   4.8  121  275-429   329-449 (593)
 18 PRK11198 hypothetical protein;  97.0  0.0023 5.8E-08   42.6   6.0   53  274-326    93-146 (147)
 19 PRK06347 autolysin; Reviewed    96.9  0.0079   2E-07   38.7   8.1  123  273-429   402-524 (593)
 20 TIGR02899 spore_safA spore coa  96.5   0.002 5.2E-08   42.9   2.6   43  281-326     1-43  (44)
 21 TIGR02907 spore_VI_D stage VI   95.6   0.015 3.8E-07   36.8   3.6   70  253-326   301-371 (371)
 22 COG1388 LytE FOG: LysM repeat   94.9   0.047 1.2E-06   33.3   4.5   46  277-327    67-112 (124)
 23 PRK09439 glucose-specific PTS   94.5    0.12 3.1E-06   30.4   5.9   79  504-585    39-124 (169)
 24 cd00210 PTS_IIA_glc PTS_IIA, P  94.4    0.14 3.5E-06   30.0   5.9   77  505-585    18-102 (124)
 25 TIGR01843 type_I_hlyD type I s  94.1   0.068 1.7E-06   32.2   3.9   24   42-66      5-28  (434)
 26 PRK11649 hypothetical protein;  94.1    0.46 1.2E-05   26.3   9.2   59  271-329   158-216 (418)
 27 pfam00358 PTS_EIIA_1 phosphoen  93.7    0.25 6.5E-06   28.1   6.2   78  505-585    23-107 (133)
 28 TIGR00830 PTBA PTS system, glu  93.6    0.19 4.8E-06   29.0   5.4   68  514-584    27-109 (129)
 29 PRK09824 beta-glucoside-specif  92.3     0.6 1.5E-05   25.5   6.4   79  504-585   495-580 (625)
 30 COG1652 XkdP Uncharacterized p  92.1    0.13 3.2E-06   30.3   2.7   50  277-327   211-263 (269)
 31 TIGR02013 rpoB DNA-directed RN  91.8    0.41   1E-05   26.7   5.1  162  411-587   658-872 (1449)
 32 PRK02597 DNA-directed RNA poly  91.5    0.51 1.3E-05   26.0   5.3   31  551-581  1028-1058(1295)
 33 TIGR02005 PTS-IIBC-alpha PTS s  91.2    0.29 7.3E-06   27.8   3.8   67  252-318   409-476 (533)
 34 TIGR01995 PTS-II-ABC-beta PTS   91.0    0.46 1.2E-05   26.3   4.7   68  514-584   538-612 (660)
 35 PRK10255 N-acetyl glucosamine   90.5     1.2 3.1E-05   23.4   6.5   85  504-591   517-613 (648)
 36 COG2190 NagE Phosphotransferas  90.4     1.2 2.9E-05   23.5   6.3   78  505-585    25-109 (156)
 37 PRK05305 phosphatidylserine de  89.5     1.4 3.6E-05   22.9   6.2   19  567-585   160-178 (214)
 38 CHL00117 rpoC2 RNA polymerase   89.2     1.6 4.1E-05   22.5   6.3   44  531-583  1080-1123(1350)
 39 COG4784 Putative Zn-dependent   88.9     1.2   3E-05   23.5   5.3   21  513-533   294-321 (479)
 40 pfam01333 Apocytochr_F_C Apocy  87.9     1.3 3.4E-05   23.0   5.1   83  524-612     3-85  (118)
 41 TIGR03309 matur_yqeB selenium-  87.4     0.8 2.1E-05   24.6   3.8   19  569-587   179-197 (256)
 42 TIGR02971 heterocyst_DevB ABC   87.1    0.55 1.4E-05   25.8   2.8   18  309-326   225-246 (363)
 43 CHL00006 consensus              86.6     1.3 3.4E-05   23.1   4.5   57    9-72    307-363 (1372)
 44 PRK05258 DNA-directed RNA poly  85.2     2.6 6.7E-05   21.0   5.5   72  508-581   952-1025(1204)
 45 TIGR02386 rpoC_TIGR DNA-direct  84.3       2 5.1E-05   21.8   4.5   66  515-581  1324-1394(1552)
 46 PRK09603 DNA-directed RNA poly  84.2     2.9 7.4E-05   20.7   6.7  108  521-636  2661-2804(2890)
 47 pfam02666 PS_Dcarbxylase Phosp  83.8       3 7.8E-05   20.5   6.3   17  570-586   153-169 (201)
 48 PRK00405 rpoB DNA-directed RNA  83.5     1.7 4.3E-05   22.4   3.8   54  521-582   647-719 (1127)
 49 PRK06302 acetyl-CoA carboxylas  83.2    0.82 2.1E-05   24.5   2.2   21  569-589   102-122 (155)
 50 PRK10260 hypothetical protein;  82.8     3.3 8.5E-05   20.3   5.3   47  277-327    41-89  (306)
 51 COG0511 AccB Biotin carboxyl c  80.2     2.4   6E-05   21.3   3.6   57  522-608    69-131 (140)
 52 PRK02693 apocytochrome f; Revi  78.8     4.5 0.00011   19.4   4.9   81  523-612   196-279 (312)
 53 CHL00001 rpoB RNA polymerase b  77.7     4.8 0.00012   19.2   4.9   57  519-583   566-635 (1065)
 54 PRK09890 cold shock protein Cs  76.8       3 7.6E-05   20.6   3.3   47  531-583     6-53  (70)
 55 cd06254 M14_ASTE_ASPA_like_4 A  76.1     2.1 5.3E-05   21.7   2.4   19  568-586   237-255 (288)
 56 PRK10190 hypothetical protein;  75.3     5.5 0.00014   18.7   4.8   47  277-327    38-86  (310)
 57 smart00357 CSP Cold shock prot  75.1     3.2 8.2E-05   20.4   3.1   39  532-575     2-43  (64)
 58 pfam00313 CSD 'Cold-shock' DNA  74.8     4.5 0.00011   19.4   3.8   49  531-584     2-50  (66)
 59 TIGR02644 Y_phosphoryl pyrimid  74.7     4.6 0.00012   19.3   3.8   57  520-586   338-405 (425)
 60 COG3835 CdaR Sugar diacid util  74.6     2.5 6.5E-05   21.1   2.5   14  389-402   327-340 (376)
 61 PRK07051 hypothetical protein;  73.3     2.6 6.7E-05   21.0   2.3   18  569-586    26-43  (80)
 62 PRK10354 major cold shock prot  73.1     5.2 0.00013   18.9   3.8   33  531-566     6-38  (70)
 63 cd06250 M14_PaAOTO_like An unc  72.6     3.2 8.1E-05   20.4   2.6   33  555-587   289-322 (359)
 64 cd06255 M14_ASTE_ASPA_like_5 A  72.3     2.9 7.5E-05   20.6   2.4   20  568-587   245-264 (293)
 65 LOAD_cold consensus             71.6     6.2 0.00016   18.4   3.9   48  531-584     3-51  (67)
 66 cd06252 M14_ASTE_ASPA_like_2 A  71.2     6.9 0.00018   18.1   4.2   21  568-588   258-278 (316)
 67 COG3858 Predicted glycosyl hyd  70.8     6.1 0.00016   18.4   3.7   53  275-331    48-100 (423)
 68 TIGR01945 rnfC electron transp  70.3     2.1 5.3E-05   21.7   1.2   17  202-218   120-136 (444)
 69 cd06251 M14_ASTE_ASPA_like_1 A  70.3     2.8 7.1E-05   20.8   1.9   18  569-586   234-251 (287)
 70 cd04458 CSP_CDS Cold-Shock Pro  70.1     6.1 0.00016   18.4   3.6   49  531-584     2-50  (65)
 71 cd06253 M14_ASTE_ASPA_like_3 A  69.6     3.7 9.3E-05   20.0   2.3   20  568-587   243-262 (298)
 72 PRK10476 multidrug resistance   69.2     7.6 0.00019   17.8   5.6   14  419-432   259-272 (348)
 73 PRK05352 Na(+)-translocating N  69.1       3 7.7E-05   20.6   1.8   16  203-218   113-128 (448)
 74 COG3170 FimV Tfp pilus assembl  68.9     7.7  0.0002   17.7   7.9   53  276-328   188-248 (755)
 75 PRK05820 deoA thymidine phosph  68.2     7.9  0.0002   17.6   3.9   57  520-586   337-404 (440)
 76 PRK10943 cold shock-like prote  67.5     6.9 0.00018   18.0   3.4   48  530-583     4-52  (69)
 77 PRK04192 V-type ATP synthase s  66.9     7.4 0.00019   17.8   3.5   22  578-599   471-492 (585)
 78 cd05830 Sortase_D_5 Sortase D   66.4     4.6 0.00012   19.3   2.3   31  541-575    42-72  (137)
 79 pfam09070 PFU PFU (PLAA family  66.3     8.6 0.00022   17.4   3.9   44  543-596     7-50  (115)
 80 PRK06078 pyrimidine-nucleoside  66.0     7.6 0.00019   17.8   3.4   57  520-586   332-399 (434)
 81 COG3608 Predicted deacylase [G  64.5     9.2 0.00024   17.2   4.8   35  569-606   271-307 (331)
 82 COG0187 GyrB Type IIA topoisom  64.5       6 0.00015   18.5   2.6   14  631-644   605-618 (635)
 83 CHL00037 petA cytochrome f      64.3     9.3 0.00024   17.1   5.0   81  523-612   203-287 (320)
 84 PRK09937 stationary phase/star  64.2     8.8 0.00023   17.3   3.4   48  531-584     3-51  (74)
 85 COG1278 CspC Cold shock protei  64.1     6.4 0.00016   18.3   2.7   43  531-576     3-49  (67)
 86 pfam00529 HlyD HlyD family sec  64.1     5.1 0.00013   19.0   2.2   26  544-576   278-303 (304)
 87 TIGR01349 PDHac_trf_mito pyruv  64.0     6.3 0.00016   18.3   2.7   13  513-525   441-453 (584)
 88 PRK09507 cspE cold shock prote  63.8     9.5 0.00024   17.1   3.6   33  531-566     5-37  (69)
 89 PRK09578 periplasmic multidrug  63.6     5.4 0.00014   18.8   2.3   14   54-67     12-25  (385)
 90 PRK09859 multidrug efflux syst  63.3     5.9 0.00015   18.5   2.4   13   55-67     11-23  (385)
 91 pfam05651 Diacid_rec Putative   62.9     5.7 0.00014   18.6   2.2   60  529-589    25-92  (135)
 92 cd06850 biotinyl_domain The bi  62.1     5.9 0.00015   18.5   2.2   20  569-588    15-34  (67)
 93 PRK05035 electron transport co  62.0     4.9 0.00012   19.1   1.8   14  204-217   131-144 (725)
 94 cd06165 Sortase_A_1 Sortase A   60.4     5.8 0.00015   18.6   1.9   56  541-612    39-95  (127)
 95 PRK11556 multidrug efflux syst  59.9     7.1 0.00018   17.9   2.3   19   40-63      7-25  (415)
 96 PRK10559 p-hydroxybenzoic acid  56.3      13 0.00032   16.2   5.3   14  313-326   201-214 (310)
 97 COG1155 NtpA Archaeal/vacuolar  55.8     9.3 0.00024   17.1   2.3   26  281-306   306-331 (588)
 98 TIGR01846 type_I_sec_HlyB type  55.7     5.9 0.00015   18.5   1.3  137  277-429   455-595 (703)
 99 PRK10218 GTP-binding protein;   54.9      12 0.00031   16.3   2.9   43  545-587   485-530 (607)
100 cd06663 Biotinyl_lipoyl_domain  53.9     9.9 0.00025   16.9   2.2   17  569-585    21-37  (73)
101 pfam00364 Biotin_lipoyl Biotin  53.9     9.9 0.00025   16.9   2.2   18  569-586    21-38  (73)
102 TIGR02472 sucr_P_syn_N sucrose  51.9     5.2 0.00013   18.9   0.5   26  494-532   354-379 (445)
103 cd06166 Sortase_D_5 Sortase D   51.6     9.7 0.00025   17.0   1.9   81  515-611    12-95  (126)
104 pfam02241 MCR_beta Methyl-coen  50.9      13 0.00032   16.2   2.4   46  511-556   155-202 (255)
105 PRK03140 phosphatidylserine de  50.1      16  0.0004   15.5   3.8   35  287-322    35-72  (259)
106 PRK03934 phosphatidylserine de  49.4     7.2 0.00018   17.9   0.9   17  568-584   250-266 (267)
107 TIGR03257 met_CoM_red_bet meth  49.3      13 0.00034   16.0   2.3   51  506-556   334-386 (433)
108 pfam10262 Rdx Rdx family. This  48.9      16 0.00042   15.4   3.7   54  546-609     2-57  (76)
109 cd00004 Sortase Sortases are c  48.8      11 0.00029   16.6   1.8   31  541-575    40-71  (128)
110 KOG3962 consensus               48.8      16 0.00042   15.4   3.7   71  512-588    73-143 (246)
111 cd05828 Sortase_D_4 Sortase D   48.5      10 0.00027   16.8   1.7   14  541-554    41-54  (127)
112 PRK05889 putative acetyl-CoA c  48.1      13 0.00034   16.0   2.1   16  569-584    55-70  (71)
113 pfam10165 Ric8 Guanine nucleot  47.6       6 0.00015   18.5   0.3   84  557-649   337-431 (438)
114 PRK04599 consensus              47.5      14 0.00037   15.8   2.2   32  552-583   251-283 (285)
115 TIGR01394 TypA_BipA GTP-bindin  46.7      17 0.00043   15.3   2.5  199  390-612   326-551 (609)
116 pfam08596 Lgl_C Lethal giant l  46.2     8.2 0.00021   17.5   0.8  142  489-645   224-391 (393)
117 PRK11160 cysteine/glutathione   46.1      15 0.00038   15.7   2.1   15  525-539   543-557 (575)
118 pfam03397 Rhabdo_matrix Rhabdo  45.6     8.1 0.00021   17.6   0.7   47  114-160    16-67  (168)
119 PTZ00265 multidrug resistance   44.7      16 0.00041   15.5   2.1   35  555-591  1172-1210(1467)
120 PRK00044 psd phosphatidylserin  44.4       7 0.00018   18.0   0.2   21  565-585   266-286 (291)
121 TIGR02203 MsbA_lipidA lipid A   44.0      15 0.00037   15.8   1.8   47  281-327   446-497 (603)
122 PRK06823 ornithine cyclodeamin  43.7      16 0.00041   15.5   2.0   14  310-323   205-218 (315)
123 PRK09282 pyruvate carboxylase   43.4      20  0.0005   14.8   4.2   17  522-538   510-526 (580)
124 PRK11892 pyruvate dehydrogenas  43.3      12 0.00029   16.5   1.2   24   93-119    27-50  (464)
125 PRK11174 cysteine/glutathione   43.0      18 0.00045   15.2   2.1   35  524-563   551-585 (588)
126 pfam07831 PYNP_C Pyrimidine nu  42.8      20 0.00051   14.8   2.5   18  569-586    38-55  (75)
127 COG4054 McrB Methyl coenzyme M  41.9      21 0.00053   14.7   2.8   54  504-557   339-394 (447)
128 pfam01887 SAM_adeno_trans S-ad  41.7      21 0.00053   14.7   4.5   22  575-603   220-241 (258)
129 cd06849 lipoyl_domain Lipoyl d  41.7      20 0.00051   14.8   2.2   29  556-584    44-74  (74)
130 PRK10125 predicted glycosyl tr  41.4      10 0.00026   16.9   0.7   40  519-569   326-365 (405)
131 cd05684 S1_DHX8_helicase S1_DH  40.3      17 0.00044   15.2   1.7   48  531-581     5-55  (79)
132 COG4656 RnfC Predicted NADH:ub  40.2      14 0.00036   15.9   1.2   23  278-300   299-321 (529)
133 TIGR01924 rsbW_low_gc anti-sig  39.9      15 0.00039   15.6   1.4   60  285-351    25-85  (161)
134 PRK08225 acetyl-CoA carboxylas  39.7      22 0.00057   14.5   2.2   15  569-583    54-68  (70)
135 TIGR03505 FimV_core FimV N-ter  39.0      23 0.00059   14.4   4.1   43  285-327     1-51  (74)
136 PRK10790 putative multidrug tr  38.9      20 0.00051   14.8   1.9   15  525-539   543-557 (593)
137 COG0845 AcrA Membrane-fusion p  38.5      23  0.0006   14.3   2.2   12  577-588   347-358 (372)
138 COG0213 DeoA Thymidine phospho  37.9      24 0.00061   14.3   3.4   57  520-586   333-400 (435)
139 pfam09449 DUF2020 Domain of un  37.6      24 0.00061   14.2   2.3   24  515-543    76-99  (144)
140 COG4181 Predicted ABC-type tra  37.5      16 0.00041   15.5   1.2   11  279-289    31-41  (228)
141 TIGR01711 gspJ general secreti  37.3      20  0.0005   14.8   1.6   16  442-457   106-121 (202)
142 KOG2525 consensus               36.9      25 0.00063   14.2   3.2   23  514-536   394-416 (496)
143 PRK05559 DNA topoisomerase IV   36.8      25 0.00063   14.1   2.7   11  632-642   607-617 (633)
144 PRK06944 sulfur carrier protei  36.6     7.6 0.00019   17.7  -0.6   49  278-326     9-59  (65)
145 PRK12727 flagellar biosynthesi  36.5      22 0.00056   14.5   1.8   25  286-310   294-318 (557)
146 PRK13657 cyclic beta-1,2-gluca  36.0      25 0.00065   14.1   2.1   52  254-313   335-386 (585)
147 smart00566 consensus            36.0      25 0.00064   14.1   2.0   11  593-603    79-89  (90)
148 PTZ00243 ABC transporter; Prov  35.9      26 0.00065   14.0   2.1   53  554-608  1313-1376(1560)
149 PRK01734 consensus              35.5      14 0.00035   15.9   0.6   34  288-322    49-86  (294)
150 COG1217 TypA Predicted membran  35.3      26 0.00067   14.0   2.7   57  541-611   480-539 (603)
151 pfam11545 HemeBinding_Shp Cell  34.9      26 0.00067   13.9   6.6   97  501-610    13-125 (151)
152 cd03245 ABCC_bacteriocin_expor  34.7      27 0.00068   13.9   2.1   24  278-302    24-47  (220)
153 COG1156 NtpB Archaeal/vacuolar  34.2      27 0.00069   13.9   5.2   29  195-223   148-176 (463)
154 COG0508 AceF Pyruvate/2-oxoglu  33.8      26 0.00066   14.0   1.8   14  616-629   376-389 (404)
155 cd03249 ABC_MTABC3_MDL1_MDL2 M  33.6      28 0.00071   13.8   2.1   14  525-538   206-219 (238)
156 COG1726 NqrA Na+-transporting   33.5      19 0.00049   14.9   1.1   17   62-78     28-44  (447)
157 TIGR00062 L27 ribosomal protei  33.4      28 0.00071   13.8   2.4   30  510-539    43-72  (83)
158 cd03228 ABCC_MRP_Like The MRP   33.2      28 0.00072   13.8   2.2   29  275-304    19-47  (171)
159 TIGR01729 taurine_ABC_bnd taur  32.7     9.7 0.00025   17.0  -0.6   13  399-411   198-210 (304)
160 PRK06549 acetyl-CoA carboxylas  32.6      29 0.00073   13.7   2.2   17  569-585   116-132 (132)
161 PRK10584 putative ABC transpor  32.5      29 0.00074   13.7   2.1   12  524-535   214-225 (228)
162 COG4615 PvdE ABC-type sideroph  32.4      20 0.00051   14.8   1.0   25  278-303   343-367 (546)
163 cd03222 ABC_RNaseL_inhibitor T  32.1      27 0.00068   13.9   1.6   22  281-303    22-43  (177)
164 TIGR01474 ubiA_proteo 4-hydrox  31.6     6.9 0.00017   18.1  -1.5   17   24-41     74-90  (291)
165 TIGR01381 E1_like_apg7 E1-like  31.4      28  0.0007   13.8   1.6  119  440-565   377-516 (689)
166 PTZ00085 40S ribosomal protein  31.3      15 0.00039   15.6   0.3   53  578-632    10-62  (67)
167 PTZ00144 dihydrolipoamide succ  30.8      31 0.00078   13.5   2.1   23  608-631   395-417 (430)
168 COG1912 Uncharacterized conser  30.4      31 0.00079   13.4   1.8   46  558-613   213-259 (268)
169 COG0444 DppD ABC-type dipeptid  29.9      32 0.00081   13.4   2.1   14  421-434   218-231 (316)
170 pfam08710 nsp9 nsp9 replicase.  29.4      32 0.00082   13.3   3.8   33  550-588    76-108 (111)
171 TIGR01348 PDHac_trf_long pyruv  29.2      31  0.0008   13.4   1.6   31  118-153    56-86  (655)
172 TIGR01437 selA_rel pyridoxal p  29.1      16  0.0004   15.5   0.0   22   51-72     66-88  (391)
173 cd03213 ABCG_EPDR ABCG transpo  29.1      33 0.00083   13.3   4.2   47  257-304     7-54  (194)
174 cd00421 intradiol_dioxygenase   28.8      33 0.00084   13.3   1.7   13  592-604    83-95  (146)
175 cd03251 ABCC_MsbA MsbA is an e  28.8      33 0.00084   13.3   2.1   11  526-536   206-216 (234)
176 KOG0215 consensus               28.7      33 0.00084   13.3   4.6  101  539-645   783-912 (1153)
177 KOG1885 consensus               28.6      33 0.00085   13.2   3.2   34  595-633   465-499 (560)
178 TIGR02408 ectoine_ThpD ectoine  28.4      17 0.00044   15.3   0.1   10  394-403   190-199 (278)
179 cd03288 ABCC_SUR2 The SUR doma  28.0      34 0.00087   13.2   2.1   44  256-303    22-65  (257)
180 cd04100 Asp_Lys_Asn_RS_N Asp_L  28.0      34 0.00087   13.2   4.6   70  534-603     2-79  (85)
181 PRK00624 glycine cleavage syst  27.9      34 0.00087   13.2   2.3   19  570-588    40-58  (113)
182 PRK10789 putative multidrug tr  27.6      35 0.00088   13.1   2.1   16  524-539   517-532 (569)
183 PRK12999 pyruvate carboxylase;  27.5      35 0.00089   13.1   2.1   16  569-584  1093-1108(1147)
184 PRK09473 oppD oligopeptide tra  27.4      35 0.00089   13.1   2.1   24  281-304   114-138 (330)
185 PTZ00109 DNA gyrase subunit b;  27.4      35 0.00089   13.1   1.6   19  398-416   624-642 (941)
186 cd03246 ABCC_Protease_Secretio  27.0      35  0.0009   13.0   2.2   30  274-304    18-47  (173)
187 PRK11022 dppD dipeptide transp  26.7      36 0.00091   13.0   2.1   13  422-434   219-231 (327)
188 pfam04203 Sortase Sortase fami  26.6      36 0.00092   13.0   2.4   28  543-575    38-65  (122)
189 pfam04017 DUF366 Domain of unk  26.5      24 0.00061   14.3   0.6   13  313-325    99-111 (183)
190 TIGR00030 S21p ribosomal prote  26.3      36 0.00093   13.0   1.9   18  278-295     2-19  (58)
191 cd02577 PSTD1 PSTD1: Pseudouri  26.1      37 0.00094   12.9   2.2   12  291-302    46-57  (319)
192 COG1038 PycA Pyruvate carboxyl  26.1      31 0.00078   13.5   1.1   23  569-591  1095-1117(1149)
193 PRK07440 hypothetical protein;  26.1      16 0.00041   15.5  -0.4   48  279-326    14-64  (70)
194 cd03247 ABCC_cytochrome_bd The  26.0      37 0.00094   12.9   2.1   29  275-304    19-47  (178)
195 cd00257 Fascin Fascin-like dom  26.0      37 0.00094   12.9   5.1   51  516-566    46-96  (119)
196 pfam06898 YqfD Putative stage   25.8      37 0.00095   12.9   3.4   10  446-455   158-167 (383)
197 COG1566 EmrA Multidrug resista  25.7      37 0.00095   12.9   4.2   21   42-63     16-36  (352)
198 COG0050 TufB GTPases - transla  25.5      33 0.00085   13.2   1.2   30  298-327   186-215 (394)
199 pfam07126 DUF1379 Protein of u  25.5      38 0.00096   12.9   4.4   51  532-584    90-140 (154)
200 COG5526 Lysozyme family protei  25.4      33 0.00084   13.3   1.1   21  409-429    65-85  (191)
201 PRK05644 gyrB DNA gyrase subun  25.3      38 0.00097   12.8   2.2   16  400-415   469-484 (725)
202 TIGR00955 3a01204 Pigment prec  25.3      38 0.00097   12.8   3.2   58  295-357   205-271 (671)
203 cd03812 GT1_CapH_like This fam  25.3      38 0.00097   12.8   2.2   39  518-567   285-323 (358)
204 PRK12835 3-ketosteroid-delta-1  25.2      38 0.00097   12.8   3.4   25  387-411   429-453 (584)
205 PRK11176 lipid transporter ATP  25.2      30 0.00076   13.6   0.9   46  255-304   342-387 (581)
206 PRK07843 3-ketosteroid-delta-1  25.1      38 0.00097   12.8   3.4   34  386-419   418-457 (560)
207 PRK03481 consensus              25.0      38 0.00098   12.8   1.5   36  552-587   253-289 (322)
208 PRK05704 dihydrolipoamide succ  25.0      38 0.00098   12.8   2.2   23  608-631   370-392 (406)
209 cd03369 ABCC_NFT1 Domain 2 of   24.9      39 0.00098   12.8   2.2   44  257-304    10-53  (207)
210 PRK04350 thymidine phosphoryla  24.7      39 0.00099   12.8   4.0   53  520-586   414-474 (502)
211 cd04949 GT1_gtfA_like This fam  24.6      23 0.00059   14.3   0.2   42  518-569   297-339 (372)
212 PRK10419 nikE nickel transport  24.6      39   0.001   12.7   2.1   10  424-433   219-228 (266)
213 cd00728 malate_synt_G Malate s  24.4     9.8 0.00025   17.0  -1.7   23  575-597   523-545 (712)
214 KOG3679 consensus               24.3     8.7 0.00022   17.3  -2.0   45  595-639   566-615 (802)
215 TIGR01172 cysE serine O-acetyl  24.3      40   0.001   12.7   1.6   14  443-456    92-105 (163)
216 PRK12839 hypothetical protein;  24.2      40   0.001   12.7   3.4   24  386-409   428-451 (574)
217 PRK09838 periplasmic copper-bi  24.2      40   0.001   12.7   3.3   27  313-339    84-110 (114)
218 COG1820 NagA N-acetylglucosami  24.1      28 0.00072   13.8   0.6   11  275-285   183-193 (380)
219 PRK08291 ornithine cyclodeamin  24.0      40   0.001   12.7   2.3   15  310-324   210-224 (330)
220 PRK11308 dppF dipeptide transp  23.8      40   0.001   12.7   2.1   11  424-434   222-232 (327)
221 PRK09099 type III secretion sy  23.6      41   0.001   12.6   6.8   26  514-539   317-342 (441)
222 TIGR01936 nqrA NADH:ubiquinone  23.5      25 0.00065   14.1   0.3   24  199-222   108-131 (466)
223 COG4729 Uncharacterized conser  23.5      41   0.001   12.6   2.9   40  571-610    87-131 (156)
224 PRK13546 teichoic acids export  23.4      41   0.001   12.6   2.1   19  290-308   109-127 (264)
225 TIGR00396 leuS_bact leucyl-tRN  23.3      37 0.00093   12.9   1.0  244  272-564   390-666 (916)
226 TIGR00986 3a0801s05tom22 mitoc  23.3      39 0.00099   12.7   1.2   25   52-76    104-128 (152)
227 COG4172 ABC-type uncharacteriz  23.2      41  0.0011   12.6   2.0   19  571-589   306-324 (534)
228 cd00164 S1_like S1_like: Ribos  23.1      42  0.0011   12.6   3.7   45  531-581     2-48  (65)
229 pfam04239 DUF421 Protein of un  23.0      42  0.0011   12.5   4.1   40  278-318     9-48  (98)
230 TIGR02465 chlorocat_1_2 chloro  23.0      40   0.001   12.7   1.2   26  287-312    15-40  (258)
231 pfam08724 Rep_N Rep protein ca  22.9      42  0.0011   12.5   1.3   11  277-287    86-96  (186)
232 PRK03695 vitamin B12-transport  22.5      43  0.0011   12.5   2.2   22  518-539   192-213 (245)
233 pfam08986 DUF1889 Domain of un  22.3      13 0.00034   16.1  -1.4   17  544-561    96-112 (119)
234 TIGR02441 fa_ox_alpha_mit fatt  22.3      43  0.0011   12.4   3.6   34  474-508   659-692 (740)
235 TIGR02645 ARCH_P_rylase putati  22.2      34 0.00086   13.2   0.7   24  289-312   212-235 (499)
236 cd00187 TOP4c DNA Topoisomeras  22.1      35 0.00089   13.1   0.7   32  130-161   132-163 (445)
237 PRK04722 consensus              22.1      44  0.0011   12.4   1.5   33  289-322    38-74  (280)
238 PRK03598 hypothetical protein;  21.8      44  0.0011   12.4   5.7   14  419-432   252-265 (331)
239 cd03795 GT1_like_4 This family  21.4      38 0.00097   12.8   0.8   29  519-547   285-314 (357)
240 cd03689 RF3_II RF3_II: this su  21.2      45  0.0012   12.3   2.4   24  572-595    59-82  (85)
241 pfam05775 AfaD Enterobacteria   21.2      45  0.0012   12.3   2.8   10  315-324    31-40  (136)
242 PRK13635 cbiO cobalt transport  21.2      45  0.0012   12.3   2.1   14  291-304   107-120 (279)
243 PRK11288 araG L-arabinose tran  21.2      45  0.0012   12.3   2.9   15  574-588   275-289 (501)
244 PRK13633 cobalt transporter AT  21.1      45  0.0012   12.3   2.1   25  290-314   111-135 (281)
245 cd03248 ABCC_TAP TAP, the Tran  21.1      45  0.0012   12.3   2.2   29  274-303    30-58  (226)
246 cd03257 ABC_NikE_OppD_transpor  21.0      46  0.0012   12.3   2.1   25  279-304    26-50  (228)
247 TIGR00848 fruA PTS system, fru  20.9      38 0.00096   12.8   0.7   43  286-329    23-65  (133)
248 COG3767 Uncharacterized low-co  20.6      46  0.0012   12.2   3.3   30   46-75      5-35  (95)
249 PRK13636 cbiO cobalt transport  20.6      46  0.0012   12.2   2.1   10  294-303   111-120 (285)
250 TIGR00078 nadC nicotinate-nucl  20.6      46  0.0012   12.2   2.2   13  299-311   107-119 (276)
251 PRK13642 cbiO cobalt transport  20.2      47  0.0012   12.2   2.1   15  291-305   107-121 (277)
252 PRK12837 3-ketosteroid-delta-1  20.2      47  0.0012   12.2   3.4   24  386-409   376-399 (515)
253 PRK05659 sulfur carrier protei  20.1      24 0.00062   14.2  -0.4   46  278-326     9-60  (66)

No 1  
>PRK11649 hypothetical protein; Provisional
Probab=100.00  E-value=0  Score=670.21  Aligned_cols=344  Identities=25%  Similarity=0.381  Sum_probs=309.4

Q ss_pred             CCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEE
Q ss_conf             64013688417970899999749998999999998540156101699888999972788864058999716883489998
Q gi|254780879|r  273 EFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIA  352 (652)
Q Consensus       273 ~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va  352 (652)
                      +.....++|++||||++||.++|++..++.+++++.   .++++|++||.|.+.++..++   +.++.+........+..
T Consensus        71 ~~~~~~y~V~~GDtLs~If~r~Gl~~~dl~~l~~~~---~~L~~LkpGq~l~~~~~~~G~---L~~L~~~~s~~e~~i~~  144 (418)
T PRK11649         71 EAGVHEYVVSTGDTLSSILNQYGIDMSDISQLAAQD---KELRNLKIGQQLSWTLTADGD---LQRLTWEVSRRETRTYD  144 (418)
T ss_pred             CCCCEEEEECCCCCHHHHHHHCCCCHHHHHHHHHCC---CCHHHCCCCCEEEEEECCCCC---EEEEEEECCCCCEEEEE
T ss_conf             777527897899809999988199999999987626---533107999989999899997---58878613765159999


Q ss_pred             ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEEEEE
Q ss_conf             42788432013332100000122111233454211025666887199989999999973011101210144540688753
Q gi|254780879|r  353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLETFFS  432 (652)
Q Consensus       353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~Vlye  432 (652)
                      +.+.+ |.       ........+++.....++|.+|||.++.++|++.++|++++++|+|+||| +++++||+|+|+|+
T Consensus       145 r~~~g-f~-------~~~~~~~~e~~~~~~~G~I~~Sl~~Sa~~aGl~~~~i~~l~~i~~~~IDF-rdlr~GD~F~Vl~e  215 (418)
T PRK11649        145 RTANG-FK-------ETSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDF-RKLKKGDEFSVLMS  215 (418)
T ss_pred             ECCCC-CE-------EEEEECCCCCCCCEEEEEECCCHHHHHHHCCCCHHHHHHHHHHHCCCCEE-EECCCCCEEEEEEE
T ss_conf             43787-21-------58753056542224799990608999988599989999999984686110-02489987999999


Q ss_pred             EECCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC-CCCCCCCCCCCCC-CCCCCCC
Q ss_conf             2115785124672368896238854201345576655444335566100000112333-4541023567641-4340443
Q gi|254780879|r  433 VNHANNQASDDSELLYIHARFGETRTRFYRFLNPVDGSVEYFNENGKSSRPFLLRTPV-PFGRMTSGFGMRY-HPILGYS  510 (652)
Q Consensus       433 ~~~~~g~~~~~geil~A~~~~~g~~~~~yrf~~~~~~~~~yyd~~G~S~~k~llr~Pv-~~~risS~Fg~R~-hPilg~~  510 (652)
                      +.+.+++. ..++|+++.+.++|+++.+|++.+   +  .|||++|+|++++|+|+|+ .+.||||+||+|| |||+|++
T Consensus       216 ~~~~dg~~-~~~~ilaa~~~~~gk~~~a~~~~d---g--~yYd~~G~sl~k~flr~P~~~~~RiSS~f~~~R~HPi~g~~  289 (418)
T PRK11649        216 REMLDGKR-EQSQLLGVRLRSGGKDYYAIRAED---G--KFYDRNGTGLAKGFLRFPTAKQFRISSNFNPRRLNPVTGRV  289 (418)
T ss_pred             EEEECCCC-CCCCEEEEEEECCCEEEEEEECCC---C--CEECCCCHHHHHHHHHCCCCCCCEECCCCCCCCEECCCCCC
T ss_conf             99846974-654089999984993799998889---9--86598766388887348666895578999898721778957


Q ss_pred             CCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCC
Q ss_conf             46420030267967279715967999653089700799983997488200214454118899788349589984166788
Q gi|254780879|r  511 RMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLS  590 (652)
Q Consensus       511 r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~S  590 (652)
                      +||+|||||||.||||+|++||+|+++||.+||||+|+|+|++||.|.|+|||+|+  |++||+|+|||+||||||||+|
T Consensus       290 ~~H~GvD~aap~GTPV~A~~dG~V~~ag~~~~yG~~V~I~H~~~~~T~Y~HLs~~~--V~~Gq~V~~Gq~Ig~vGsTG~s  367 (418)
T PRK11649        290 APHRGVDFAMPQGTPVLSVGDGEVVVAKRSGAAGNYVAIRHGRQYTTRYMHLRKLL--VKPGQKVKRGDRIALSGNTGRS  367 (418)
T ss_pred             CCCCCCCCCCCCCCEEEEECCEEEEEEEECCCCCCEEEEECCCCEEEEEECCCCCC--CCCCCEECCCCEEEEECCCCCC
T ss_conf             55367566676899898524879999788189997799981993099961768477--7994999989989802688378


Q ss_pred             CCCEEEEEEEECCEECCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8742688997867883662000788787888999999999999999984
Q gi|254780879|r  591 TGPHLHYELIVNGIKVDSTKVRIPERENLKGDLLQRFAMEKKRINSLLN  639 (652)
Q Consensus       591 TGPHLHfEv~vnG~~VdP~~~~lp~~~~l~~~~l~~F~~~~~~id~ll~  639 (652)
                      |||||||||++||++||||+++||.+++|+++++++|+++...+-+.|.
T Consensus       368 TGPHLHyEv~~ng~~vnPl~vklP~~~~l~~~e~~~F~~~~~~~~~~L~  416 (418)
T PRK11649        368 TGPHLHYEVWINQQAVNPLTAKLPRTEGLTGSDRREYLAQVKEVVPQLR  416 (418)
T ss_pred             CCCEEEEEEEECCEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             8973389999999795995346889997898999999999999999753


No 2  
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=1.4e-45  Score=339.58  Aligned_cols=141  Identities=47%  Similarity=0.860  Sum_probs=131.8

Q ss_pred             CCCCCCCCHHHCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEEC-CCCCEEEE
Q ss_conf             3355661000001123334--54102356764143404434642003026796727971596799965308-97007999
Q gi|254780879|r  473 YFNENGKSSRPFLLRTPVP--FGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAG-GYGKQTLI  549 (652)
Q Consensus       473 yyd~~G~S~~k~llr~Pv~--~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~-GyGn~V~I  549 (652)
                      +++..+.+.....+++|++  .++|+|.||+|.||+++..++|+||||++|.||||+|+++|+|+++|+.+ +|||+|+|
T Consensus       121 ~~~~~~~~~~~~~~~~p~~~~~~~i~s~fg~r~~p~~~~~~~h~GiD~aa~~gtpV~A~~~G~V~~~~~~~~~yGn~v~i  200 (277)
T COG0739         121 AYDVGGKLLELFGLRWPLPNGKGKISSGFGRRIHPVTGRLEPHKGIDIAAPEGTPVYAAADGVVVFAGNGGWGYGNLVII  200 (277)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEECCCCCCEEEECCCEEEEEECCCCCCCCEEEEE
T ss_conf             11335442112000056667786386567765355556546778805026899867851681899970476667708999


Q ss_pred             ECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCE---ECCCCEECCCCC
Q ss_conf             8399748820021445411889978834958998416678887426889978678---836620007887
Q gi|254780879|r  550 HHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGI---KVDSTKVRIPER  616 (652)
Q Consensus       550 ~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~---~VdP~~~~lp~~  616 (652)
                      +|++||+|.|+|||++.  |+.||+|++||+||+||+||+||||||||||++||+   ++||+.. |+..
T Consensus       201 ~H~~g~~t~Y~Hl~~~~--V~~G~~V~~G~~Ig~~G~tG~stgphLHfev~~~g~~~~~~~p~~~-l~~~  267 (277)
T COG0739         201 KHGDGYVTVYAHLSSIL--VKEGQKVKAGQVIGYVGSTGRSTGPHLHFEVRKNGKLVPPVNPARY-LPKG  267 (277)
T ss_pred             ECCCCEEEEEECCCCCC--CCCCCEEECCCEEEECCCCCCCCCCEEEEEEEECCCCCCCCCHHHH-CCCC
T ss_conf             74896588996065013--1589788469789972576775797588988758703675785562-2444


No 3  
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=100.00  E-value=1.5e-43  Score=325.28  Aligned_cols=119  Identities=34%  Similarity=0.592  Sum_probs=110.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-CCCCCEEEEECCCCEEEEEHHHH
Q ss_conf             11233345410235676414340443464200302679672797159679996530-89700799983997488200214
Q gi|254780879|r  485 LLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-GGYGKQTLIHHGNGYVSSYNHQD  563 (652)
Q Consensus       485 llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-~GyGn~V~I~H~~Gy~T~YaHlS  563 (652)
                      -++||+.+ ++...|+.+...       |+||||+++.|+||+|+++|+|+|+|+. .||||+|+|+|+++|.|+|+|++
T Consensus       254 ~W~WP~~G-kVi~~Fs~~~~g-------nkGidia~~~G~pV~Aaa~G~VvyaG~~l~gyGnliiIkH~~~~lsaYahn~  325 (374)
T PRK10871        254 TWRWPTDG-KVIENFGASEGG-------NKGIDIAGSKGQAIIATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHND  325 (374)
T ss_pred             CCCCCCCC-CCCCCCCCCCCC-------CCEEEEECCCCCEEEECCCEEEEEECCCCCCCCEEEEEECCCCCEEEEECCC
T ss_conf             34377898-685404777788-------6507985789981785378389992478787762899984998678616766


Q ss_pred             HHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCEECCCC
Q ss_conf             4541188997883495899841667888742688997867883662000788
Q gi|254780879|r  564 AIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKVRIPE  615 (652)
Q Consensus       564 ~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~~lp~  615 (652)
                      ++.  |++||+|++||+||.||+||.++ ||||||||++|++||||+. ||+
T Consensus       326 ~~l--Vkeg~~V~~Gq~Ia~~G~tg~~~-~~LHFEiR~~g~pvdP~~y-LPk  373 (374)
T PRK10871        326 TML--VREQQEVKAGQKIATMGSTGTSS-TRLHFEIRYKGKSVNPLRY-LPQ  373 (374)
T ss_pred             CCC--CCCCCEECCCCEEEEECCCCCCC-CEEEEEEEECCEECCHHHH-CCC
T ss_conf             266--78889988999898643789998-3089999779986694897-649


No 4  
>PRK11637 hypothetical protein; Provisional
Probab=100.00  E-value=2e-44  Score=331.51  Aligned_cols=121  Identities=29%  Similarity=0.460  Sum_probs=113.8

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHH
Q ss_conf             00112333454102356764143404434642003026796727971596799965308970079998399748820021
Q gi|254780879|r  483 PFLLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQ  562 (652)
Q Consensus       483 k~llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHl  562 (652)
                      +..+.||+ .|+++++||.++||.+    .|+||||+++.||||+|+.+|+|+|++|.+||||+|+|+|+|||.|.|+||
T Consensus       280 ~G~l~wPv-~G~i~~~fG~~~~~~~----~~~GidI~a~~Gt~V~Av~~G~Vv~a~~~~gyG~~ViIdHG~g~~TlYah~  354 (404)
T PRK11637        280 RGQAFWPV-RGPTLHRYGEQLQGEL----RWKGMVIGASEGTEVKAIADGRVILADWLQGYGLVVVVEHGKGDMSLYGYN  354 (404)
T ss_pred             CCCCCCCC-CCCCCCCCCCCCCCCC----CCCCEEEECCCCCEEEEECCEEEEEEEECCCCCCEEEEECCCCCEEECCCC
T ss_conf             89857687-7770467899999977----758758756999805410176999911408888579998699465715288


Q ss_pred             HHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCE
Q ss_conf             445411889978834958998416678887426889978678836620
Q gi|254780879|r  563 DAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTK  610 (652)
Q Consensus       563 S~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~  610 (652)
                      |++.  |++||+|++||+||+||+||.|||||||||||+||+|||||.
T Consensus       355 s~l~--v~~Gq~V~~Gq~Ig~vG~tG~s~g~~LhFEir~~g~~vnP~~  400 (404)
T PRK11637        355 QSAL--VSVGAQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQP  400 (404)
T ss_pred             CCCC--CCCCCEECCCCEEEEEECCCCCCCCEEEEEEEECCEEECHHH
T ss_conf             9588--899799899996987326899999658999998999847588


No 5  
>pfam01551 Peptidase_M23 Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.
Probab=99.97  E-value=2.8e-30  Score=231.90  Aligned_cols=96  Identities=53%  Similarity=0.934  Sum_probs=94.3

Q ss_pred             CCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCC
Q ss_conf             46420030267967279715967999653089700799983997488200214454118899788349589984166788
Q gi|254780879|r  511 RMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLS  590 (652)
Q Consensus       511 r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~S  590 (652)
                      |+|+||||+++.|+||+|+.+|+|++++|..+||++|+|+|++||.|.|+||+++.  |++||+|++||+||++|++|.+
T Consensus         1 ~~H~GiDi~~~~G~~V~A~~~G~V~~~~~~~~~G~~v~i~h~~g~~~~Y~hl~~~~--V~~G~~V~~G~~IG~~G~sg~~   78 (96)
T pfam01551         1 RFHKGIDIAAPTGTPVYAAADGVVVFAGYLGGYGNLVIIDHGNGYETLYAHLSKIL--VKVGQRVKAGQVIGTVGSTGRS   78 (96)
T ss_pred             CCCCCEEECCCCCCEEEEEECEEEEEEEECCCCCEEEEEEECCCCEEEECCCEEEE--ECCCCCHHHCCEEEEECCCCCC
T ss_conf             93228984658999899623679999898399885999993898769983644677--9589890139999986789998


Q ss_pred             CCCEEEEEEEECCEECCC
Q ss_conf             874268899786788366
Q gi|254780879|r  591 TGPHLHYELIVNGIKVDS  608 (652)
Q Consensus       591 TGPHLHfEv~vnG~~VdP  608 (652)
                      +|||||||||++|++|||
T Consensus        79 ~~~hLHfei~~~~~~vdP   96 (96)
T pfam01551        79 TGPHLHFEIRKNGKPVDP   96 (96)
T ss_pred             CCEEEEEEEEECCEECCC
T ss_conf             980899999999999877


No 6  
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=99.94  E-value=2.5e-27  Score=211.05  Aligned_cols=128  Identities=30%  Similarity=0.465  Sum_probs=112.6

Q ss_pred             CCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCE
Q ss_conf             56610000011233345410235676414340443464200302679672797159679996530897007999839974
Q gi|254780879|r  476 ENGKSSRPFLLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGY  555 (652)
Q Consensus       476 ~~G~S~~k~llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy  555 (652)
                      ..|-+..+.-+.|||.+ +|.-.||-..--    ...-+|+-|+++.|++|.|.+||+|+||||..|||.+|+|+|++||
T Consensus       289 t~~~~~~~G~l~~PV~G-~il~rFG~~~~g----g~~wkG~vi~a~~Ga~V~A~AdG~VvyA~~l~GYG~vvIldhG~gy  363 (420)
T COG4942         289 TGGFGALRGQLAWPVTG-RILRRFGQADGG----GLRWKGMVIGASAGATVKAIADGRVVYADWLRGYGLVVILDHGGGY  363 (420)
T ss_pred             CCCCCCCCCCCCCCCCC-HHHHHHCCCCCC----CCCCCCEEEECCCCCEEEECCCCEEEECHHHCCCCEEEEEECCCCC
T ss_conf             55320025776888787-078773456788----7610675873599982562069569954332567569999748853


Q ss_pred             EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCE
Q ss_conf             8820021445411889978834958998416678887426889978678836620
Q gi|254780879|r  556 VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTK  610 (652)
Q Consensus       556 ~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~  610 (652)
                      .+.|+||+.+.  |++|+.|+.||.||.||++|-..-|-|+||||.||+||||..
T Consensus       364 ~slyg~~~~i~--v~~G~~V~AGepIa~~G~sgg~~~p~LYfEiR~~G~pvnP~p  416 (420)
T COG4942         364 HSLYGGNQSIL--VNPGQFVKAGEPIALVGSSGGQGRPALYFEIRRQGQPVNPQP  416 (420)
T ss_pred             EEEECCCCEEE--ECCCCEEECCCCHHHCCCCCCCCCCCHHHHHHHCCCCCCCHH
T ss_conf             78861664221--068977556971532267789998410021460597479512


No 7  
>PRK06148 hypothetical protein; Provisional
Probab=99.49  E-value=1.2e-13  Score=114.86  Aligned_cols=102  Identities=27%  Similarity=0.493  Sum_probs=84.3

Q ss_pred             CCCCCCEEECCCCCCCEEECCCCEEEEEEEE---CCCCCEEEEECC--CC--EEEEEHHHHHHH-HCCCCCCEEECCCEE
Q ss_conf             3464200302679672797159679996530---897007999839--97--488200214454-118899788349589
Q gi|254780879|r  510 SRMHTGVDWAAPRGTPIVAVGDGIVEKANWA---GGYGKQTLIHHG--NG--YVSSYNHQDAIA-KNIKAGTAVKQGQII  581 (652)
Q Consensus       510 ~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~---~GyGn~V~I~H~--~G--y~T~YaHlS~~a-~gV~~G~~V~qGQvI  581 (652)
                      .-.|.|||+=+|.||||+|.-+|+|+.+..+   -+||-.|+++|.  +|  +.|.|+||+.-. ..+++|++|++||.|
T Consensus       440 RTihLGVDl~~p~gT~V~AP~dG~V~~~~n~~~~l~yGg~iiL~h~~~~~~~F~tLyGhl~~~~~~~l~~G~~i~~G~~i  519 (1015)
T PRK06148        440 RTVHLGVDLFMPAGTPVYAPLAGTVRSVEIEAVPLGYGGLIALEHEPPGCPPFYTLWGHLAHEAVSRLKPGDRLAAGELV  519 (1015)
T ss_pred             CEEEEEEEEEECCCCCEECCCCCEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCEE
T ss_conf             32654257750699804466586699962476555677548998425888750565235772553126888850467712


Q ss_pred             EEECCCCCCCC--CEEEEEEEE--CCEECCCCEE
Q ss_conf             98416678887--426889978--6788366200
Q gi|254780879|r  582 GWIGTTGLSTG--PHLHYELIV--NGIKVDSTKV  611 (652)
Q Consensus       582 G~vGsTG~STG--PHLHfEv~v--nG~~VdP~~~  611 (652)
                      |.+|+....-|  |||||.+.-  .|...|+-.+
T Consensus       520 g~~G~~~~nggw~phlh~Ql~~~~~~~~~~~Pgv  553 (1015)
T PRK06148        520 GHMGDAHENGGWAPHLHFQISTDTQLSATEILGV  553 (1015)
T ss_pred             EECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCC
T ss_conf             3426654468877615898851345678889885


No 8  
>PRK06149 hypothetical protein; Provisional
Probab=98.93  E-value=2.8e-09  Score=84.10  Aligned_cols=80  Identities=20%  Similarity=0.191  Sum_probs=68.9

Q ss_pred             CCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCC
Q ss_conf             34642003026796727971596799965308970079998399748820021445411889978834958998416678
Q gi|254780879|r  510 SRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGL  589 (652)
Q Consensus       510 ~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~  589 (652)
                      .-.|.|||+=+|.||||+|.-+|+|.     ..||.+|.++|+.-..|.|+++..    ++.|++|+.||.||..++.| 
T Consensus       429 rTvhLGvDl~~pagTpV~AP~~G~V~-----~~~~g~~~l~~~~~~~~L~g~~~~----~~~g~~i~~G~~ig~~~~~g-  498 (972)
T PRK06149        429 ATCALGVELWLAAGTAVAAPFAGEIG-----RDGDGRLTLRGDAWELHLTGVEPA----VADGAAVEAGQPLGSASALG-  498 (972)
T ss_pred             CEEEEEEEEEECCCCEEECCCCCEEE-----ECCCCEEEEECCCEEEEEECCCCC----CCCCCEEECCCCCCCCCCCC-
T ss_conf             50430045660799805466576699-----716964898517548998256776----67767520677003366688-


Q ss_pred             CCCCEEEEEEEECC
Q ss_conf             88742688997867
Q gi|254780879|r  590 STGPHLHYELIVNG  603 (652)
Q Consensus       590 STGPHLHfEv~vnG  603 (652)
                          ||||.+.-..
T Consensus       499 ----~l~~ql~~~~  508 (972)
T PRK06149        499 ----FLRVQLCPVA  508 (972)
T ss_pred             ----CEEEEEECCC
T ss_conf             ----4799972167


No 9  
>pfam04225 OapA Opacity-associated protein A LysM-like domain. This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation. This is a LysM-like domain.
Probab=98.61  E-value=6.9e-07  Score=67.30  Aligned_cols=82  Identities=9%  Similarity=0.134  Sum_probs=68.3

Q ss_pred             EEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEEECC
Q ss_conf             13688417970899999749998999999998540156101699888999972788864058999716883489998427
Q gi|254780879|r  276 DDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIALND  355 (652)
Q Consensus       276 e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~d  355 (652)
                      ++.++|++||||+.|++++|++..|+++++++-.....+.+|++||.+++.....+   ++..+.+..+ ...+...+..
T Consensus         2 W~~y~V~~GdTLs~iFr~~~L~~sDv~~~~~~~g~~k~Ls~Lk~Gq~v~~~~n~~G---~l~~L~i~~~-~~~v~f~R~~   77 (85)
T pfam04225         2 WKTYQVPKGDTLMQVFRDNNLPISDVNAMAKVEGADKPLSNIKSGQLVRIKLNAQG---RVDELQIENG-AGSVMFFRQS   77 (85)
T ss_pred             CEEEEECCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHCCCCCEEEEEECCCC---CEEEEEEECC-CEEEEEEECC
T ss_conf             70678079985999998829998999999861156780544589999999999999---8899998149-9489999818


Q ss_pred             CCCEEE
Q ss_conf             884320
Q gi|254780879|r  356 NNEYVL  361 (652)
Q Consensus       356 ~g~fv~  361 (652)
                      +|.|..
T Consensus        78 DGsf~r   83 (85)
T pfam04225        78 DGSFGR   83 (85)
T ss_pred             CCCEEE
T ss_conf             986452


No 10 
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=98.11  E-value=5.9e-05  Score=53.68  Aligned_cols=108  Identities=17%  Similarity=0.166  Sum_probs=72.5

Q ss_pred             CCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEE
Q ss_conf             64013688417970899999749998999999998540156101699888999972788864058999716883489998
Q gi|254780879|r  273 EFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIA  352 (652)
Q Consensus       273 ~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va  352 (652)
                      ....+.+.||+||||+.|.+++|++..++.++    |+.. .+.|++||.|.|+.........      ...        
T Consensus       340 ~~~~~~y~Vr~GDtL~~IA~ky~vsv~~L~~~----N~L~-~~~L~~Gq~L~Ip~~~~~~~~~------~~~--------  400 (449)
T PRK10783        340 PLNSRSYKVRSGDTLSGIASRLGVSTKDLQQW----NNLR-GSTLKVGQSLTIGAGSSAQRLA------NNS--------  400 (449)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHCCCHHHHHHH----CCCC-CCCCCCCCEEEECCCCCCCCCC------CCC--------
T ss_conf             56760588589998999999979799999998----3999-4447899878737887555565------678--------


Q ss_pred             ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEEEE
Q ss_conf             4278843201333210000012211123345421102566688719998999999997301110121014454068875
Q gi|254780879|r  353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLETFF  431 (652)
Q Consensus       353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~Vly  431 (652)
                                 .+.              .-...-.||||..|.+++++..-+.+...+       ...+++|+++.+..
T Consensus       401 -----------~~~--------------~Y~Vk~GDTL~~IArry~Vsv~~L~~wN~~-------~~~L~pGQkL~I~v  447 (449)
T PRK10783        401 -----------DSI--------------TYRVRKGDSLSSIAKRHGVNIKDVMRWNSD-------TANLQPGDKLTLFV  447 (449)
T ss_pred             -----------CCE--------------EEEECCCCCHHHHHHHHCCCHHHHHHHCCC-------CCCCCCCCEEEEEE
T ss_conf             -----------965--------------899899997999999969899999986599-------77878999889984


No 11 
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=98.02  E-value=0.00017  Score=50.45  Aligned_cols=83  Identities=8%  Similarity=0.134  Sum_probs=70.7

Q ss_pred             CEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEEEC
Q ss_conf             01368841797089999974999899999999854015610169988899997278886405899971688348999842
Q gi|254780879|r  275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIALN  354 (652)
Q Consensus       275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~  354 (652)
                      .++.++|.+|+||..++++++++..|+.++++.-..-..+.+|+.||.++|.....|   ++..+.+..+.. ++...+-
T Consensus       158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~naqG---~Vt~L~le~~n~-~vlF~RQ  233 (242)
T COG3061         158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNAQG---RVTELRLETGNN-QVLFTRQ  233 (242)
T ss_pred             CCEEEEECCCCCHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHCCCCCEEEEEECCCC---CEEEEEECCCCC-EEEEEEC
T ss_conf             651587168765999876069985776787753047870222147777999974766---457899616985-4889972


Q ss_pred             CCCCEEE
Q ss_conf             7884320
Q gi|254780879|r  355 DNNEYVL  361 (652)
Q Consensus       355 d~g~fv~  361 (652)
                      .+|.|..
T Consensus       234 ~DGSy~r  240 (242)
T COG3061         234 SDGSYIR  240 (242)
T ss_pred             CCCCCCC
T ss_conf             7886222


No 12 
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=97.76  E-value=0.00011  Score=51.78  Aligned_cols=122  Identities=13%  Similarity=0.051  Sum_probs=55.9

Q ss_pred             EEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCE--EEEEECCCCCCCEEEEEEECCCCCEEEEEEEC
Q ss_conf             3688417970899999749998999999998540156101699888--99997278886405899971688348999842
Q gi|254780879|r  277 DLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEI--LRIGVVQKDDKFTIVRFSIYHKQKHLLTIALN  354 (652)
Q Consensus       277 ~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~--L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~  354 (652)
                      ..|.|..+-.|..+++-.|++.+++.+.    |..++-....++..  |.|+......   +. ..+...     .++  
T Consensus       264 ~~V~v~~~idL~~~A~~agi~~~~l~~L----NP~~~r~~t~p~g~~~lllP~~~~~~---f~-~~l~~~-----~~~--  328 (449)
T PRK10783        264 ARVDLGSPVELAQVADMAGMSLSKLKTF----NAGVKGSTLGPSGPQYVMVPKKHAEQ---LR-ESLASG-----EIA--  328 (449)
T ss_pred             EEEECCCCCCHHHHHHHHCCCHHHHHHH----CHHHCCCCCCCCCCCEEECCHHHHHH---HH-HHHHCC-----CHH--
T ss_conf             9994699866999998819799999985----86517787689998568683799999---99-986122-----122--


Q ss_pred             CCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE
Q ss_conf             788432013332100000122111233454211025666887199989999999973011101210144540688
Q gi|254780879|r  355 DNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET  429 (652)
Q Consensus       355 d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V  429 (652)
                             ...+...... ..  .........-.++|+..|.+.+++...+.+..++-+      ..++.|..+.|
T Consensus       329 -------~~~~~~~~~~-~~--~~~~~y~Vr~GDtL~~IA~ky~vsv~~L~~~N~L~~------~~L~~Gq~L~I  387 (449)
T PRK10783        329 -------AVQSTLVADN-TP--LNSRSYKVRSGDTLSGIASRLGVSTKDLQQWNNLRG------STLKVGQSLTI  387 (449)
T ss_pred             -------HCCCCCCCCC-CC--CCCEEEEECCCCCHHHHHHHHCCCHHHHHHHCCCCC------CCCCCCCEEEE
T ss_conf             -------2143100112-45--676058858999899999997979999999839994------44789987873


No 13 
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=97.60  E-value=9.8e-05  Score=52.16  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=40.4

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE
Q ss_conf             6884179708999997499989999999985401561016998889999
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG  326 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~  326 (652)
                      .++|++||||++|+.++|++..++.++    |+..+.+.|++||+|.|+
T Consensus         2 ~y~V~~GDTl~~Ia~~~~v~~~~l~~~----N~~~~~~~l~~Gq~l~iP   46 (46)
T cd00118           2 TYTVKKGDTLSSIAQRYGISVEELLKL----NGLSDPDNLQVGQKLKIP   46 (46)
T ss_pred             EEEECCCCCHHHHHHHHCCCHHHHHHH----CCCCCCCCCCCCCEEEEC
T ss_conf             479898999999999989679999986----699997716769999609


No 14 
>smart00257 LysM Lysin motif.
Probab=97.53  E-value=0.00012  Score=51.59  Aligned_cols=44  Identities=20%  Similarity=0.252  Sum_probs=39.1

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEE
Q ss_conf             688417970899999749998999999998540156101699888999
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRI  325 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I  325 (652)
                      .++|++||||++|..+||++..++.++    |+..+.+.|++||+|.|
T Consensus         1 ty~V~~GDTl~~IA~~~~v~~~~l~~~----N~~~~~~~l~~Gq~l~I   44 (44)
T smart00257        1 TYTVKKGDTLSSIARRYGISVSDLLEL----NNILDPDNLQVGQKLKI   44 (44)
T ss_pred             CCEECCCCCHHHHHHHHCCCHHHHHHH----CCCCCCCCCCCCCEEEC
T ss_conf             908798988999999989689999987----69999772487999859


No 15 
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=97.27  E-value=0.00055  Score=46.91  Aligned_cols=43  Identities=14%  Similarity=0.251  Sum_probs=19.5

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEE
Q ss_conf             688417970899999749998999999998540156101699888999
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRI  325 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I  325 (652)
                      .|+||+||||++|..+||++.+++.++    |++ ..+.|.|||+|.|
T Consensus        27 TytVksGDTLW~IA~kygvSVa~Lks~----NnL-~SD~I~pGQkL~V   69 (475)
T PRK13914         27 TVVVEAGDTLWGIAQSKGTTVDAIKKA----NNL-TTDKIVPGQKLQV   69 (475)
T ss_pred             EEEECCCCCHHHHHHHHCCCHHHHHHH----HCC-CCCEEECCCEEEE
T ss_conf             889657985899898819889999997----588-7670506877986


No 16 
>pfam01476 LysM LysM domain. The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known.
Probab=97.24  E-value=0.00041  Score=47.77  Aligned_cols=43  Identities=14%  Similarity=0.165  Sum_probs=36.3

Q ss_pred             EEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE
Q ss_conf             884179708999997499989999999985401561016998889999
Q gi|254780879|r  279 IPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG  326 (652)
Q Consensus       279 v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~  326 (652)
                      ++|++||||+.|.+++|++.+++.++    |+. ....|++||.|.|+
T Consensus         1 y~V~~GDtl~~IA~~~~v~~~~i~~~----N~l-~~~~i~~Gq~l~IP   43 (43)
T pfam01476         1 YTVKKGDTLSSIAKRYGITVEELAEL----NGL-SSPNLYVGQKLKIP   43 (43)
T ss_pred             CEECCCCCHHHHHHHHCCCHHHHHHH----HCC-CCCCCCCCCEEECC
T ss_conf             98798987999999989689999998----589-99856889998539


No 17 
>PRK06347 autolysin; Reviewed
Probab=97.03  E-value=0.0011  Score=44.66  Aligned_cols=121  Identities=8%  Similarity=0.070  Sum_probs=66.0

Q ss_pred             CEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEEEC
Q ss_conf             01368841797089999974999899999999854015610169988899997278886405899971688348999842
Q gi|254780879|r  275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIALN  354 (652)
Q Consensus       275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va~~  354 (652)
                      .-..++|+.||||+.|..+||++.......    ++..+ +.|-+||.|.+............     ....   ....+
T Consensus       329 as~tYTV~sGDTl~~IA~KyGtSV~~L~sw----N~is~-~~IY~GQ~L~V~~~s~stnt~~s-----~~nt---~~n~n  395 (593)
T PRK06347        329 NAKIYTVVKGDSLWRIANNHKVTVANLKAW----NNLKS-DFIYPGQKLKVSAGSTTSNTNTS-----KPST---GTSTS  395 (593)
T ss_pred             CCCEEEEECCCCHHHHHHCCCCCHHHHHHH----HCCCC-CCEECCCEEEECCCCCCCCCCCC-----CCCC---CCCCC
T ss_conf             564589844868888763155148777776----46567-84331767887467666666667-----7764---54445


Q ss_pred             CCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE
Q ss_conf             788432013332100000122111233454211025666887199989999999973011101210144540688
Q gi|254780879|r  355 DNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET  429 (652)
Q Consensus       355 d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V  429 (652)
                                     ................-.|+||..+.+++++-+-+..+.++-   -||   |.+|..++|
T Consensus       396 ---------------~~~tsstTsa~tYTVkSGDTLw~IA~K~g~SV~~LkswNnLs---sd~---IYpGQvLkV  449 (593)
T PRK06347        396 ---------------KPSTSTSTNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLK---SDF---IYPGQKLKV  449 (593)
T ss_pred             ---------------CCCCCCCCCCEEEEEECCCCHHHHHHHCCCCHHHHHHHCCCC---CCE---EEECCEEEE
T ss_conf             ---------------567765433127998228758877741595789975440666---766---863307998


No 18 
>PRK11198 hypothetical protein; Provisional
Probab=96.98  E-value=0.0023  Score=42.56  Aligned_cols=53  Identities=17%  Similarity=0.119  Sum_probs=37.3

Q ss_pred             CCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHC-CCCHHHCCCCCEEEEE
Q ss_conf             4013688417970899999749998999999998540-1561016998889999
Q gi|254780879|r  274 FADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKN-EVRVDQLTKDEILRIG  326 (652)
Q Consensus       274 ~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~-~~~~~~Lr~Gq~L~I~  326 (652)
                      .+.+.++|++||||++|.+++=-+...-.+|.++-+. ..+.+.|.|||.|+|+
T Consensus        93 ~e~~~YtVq~GDTLw~IA~k~YGd~~~~~~I~eANk~~I~nPd~IyPGQvL~IP  146 (147)
T PRK11198         93 PESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP  146 (147)
T ss_pred             CCCCEEEECCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEECC
T ss_conf             998578979899799999998398878999999616508995841899988378


No 19 
>PRK06347 autolysin; Reviewed
Probab=96.88  E-value=0.0079  Score=38.74  Aligned_cols=123  Identities=10%  Similarity=0.078  Sum_probs=66.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEEEE
Q ss_conf             64013688417970899999749998999999998540156101699888999972788864058999716883489998
Q gi|254780879|r  273 EFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKFTIVRFSIYHKQKHLLTIA  352 (652)
Q Consensus       273 ~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~~~~r~si~~~~~~~~~va  352 (652)
                      ...-+.++|+.||||+.|..++|++..++..+    +++.. +-|.+||.|.+.-.............  ......    
T Consensus       402 tTsa~tYTVkSGDTLw~IA~K~g~SV~~Lksw----NnLss-d~IYpGQvLkVs~~ssss~snts~~~--t~s~ss----  470 (593)
T PRK06347        402 STNAKVYTVVKGDSLWRIANNNKVTIANLKSW----NNLKS-DFIYPGQKLKVSAGSTTSNTNTSKPS--TNTNTS----  470 (593)
T ss_pred             CCCCEEEEEECCCCHHHHHHHCCCCHHHHHHH----CCCCC-CEEEECCEEEECCCCCCCCCCCCCCC--CCCCCC----
T ss_conf             43312799822875887774159578997544----06667-66863307998056556887766655--455433----


Q ss_pred             ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE
Q ss_conf             42788432013332100000122111233454211025666887199989999999973011101210144540688
Q gi|254780879|r  353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET  429 (652)
Q Consensus       353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V  429 (652)
                                    .   ...............-.++||..+.++|+.-.-+..   ++.-.-|+   +.+|..++|
T Consensus       471 --------------~---~ss~tstsastYTVksGDSLw~IA~K~GtSV~~L~s---wNniksd~---Iy~GQkLkV  524 (593)
T PRK06347        471 --------------K---PSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLKS---WNNLKSDF---IYPGQKLKV  524 (593)
T ss_pred             --------------C---CCCCCCCCCEEEEECCCCCHHHHHHHCCCCHHHHHH---HHCCCCCC---EEECEEEEE
T ss_conf             --------------5---566554454069983685378888770841777555---52457773---350407997


No 20 
>TIGR02899 spore_safA spore coat assembly protein SafA; InterPro: IPR014248   This entry represents a domain of about 40 residues long which is found in a variety of enzymes involved in bacterial cell wall degradation , and which may have a general peptidoglycan binding function. Proteins containing this domain include SafA of Bacillus subtilis, which is a protein found at the interface of the spore cortex and spore coat, and which is dependent on SpoVID for its localization. This domain is generally found towards the N-terminus of these proteins. The C-terminal region of these proteins are more variable and may contain blocks of 12-residue and 13-residue repeats, tandem LysM domains (IPR002482 from INTERPRO), or an SCP-like domain (IPR014258 from INTERPRO)..
Probab=96.46  E-value=0.002  Score=42.88  Aligned_cols=43  Identities=9%  Similarity=0.092  Sum_probs=36.9

Q ss_pred             ECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE
Q ss_conf             4179708999997499989999999985401561016998889999
Q gi|254780879|r  281 IQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG  326 (652)
Q Consensus       281 VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~  326 (652)
                      |++||||.+|+.+|||+-+++.++   -..+.+.+-+-||++|.|+
T Consensus         1 Vq~GDtlWkiA~kygV~~~~Li~~---NpQl~nP~~IyPG~ki~IP   43 (44)
T TIGR02899         1 VQKGDTLWKIAKKYGVDLDELIQA---NPQLSNPNLIYPGMKIKIP   43 (44)
T ss_pred             CCCCCHHHHHHHHHCCCHHHHHHH---CCCCCCCCCCCCCCEECCC
T ss_conf             998821477787717876788641---6887888834899511078


No 21 
>TIGR02907 spore_VI_D stage VI sporulation protein D; InterPro: IPR014256   This entry represents SpoVID, the stage VI sporulation protein D, which is restricted to endospore-forming bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich in glutamic acid. SpoVID is involved in spore coat assembly in the mother cell compartment late in the process of sporulation..
Probab=95.55  E-value=0.015  Score=36.79  Aligned_cols=70  Identities=14%  Similarity=0.070  Sum_probs=49.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC-CCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE
Q ss_conf             122334222665445677776-40136884179708999997499989999999985401561016998889999
Q gi|254780879|r  253 KIIEENRTITSPQVLIDKIPE-FADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG  326 (652)
Q Consensus       253 ~~~~en~t~~~~~~~~~~~~~-~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~  326 (652)
                      .--+||++-.+.--....--. +..|+..|+.||||.+|+.||-+++..+.++    |++-....+..||.|.|+
T Consensus       301 ~~r~Ena~YLt~lf~~~eeE~FTKlk~civQe~dtle~IA~RY~~S~~qL~r~----N~leSD~~v~~GQlLYIP  371 (371)
T TIGR02907       301 KEREENALYLTKLFAKEEEEEFTKLKMCIVQEGDTLETIAERYEVSVSQLLRV----NQLESDEEVNEGQLLYIP  371 (371)
T ss_pred             CCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECCCCHHHHHHHHCCCHHHHHHH----CCCCCCHHHCCCCEEECC
T ss_conf             78760255777875048432100038889852886554540212586887520----365572335175145219


No 22 
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=94.91  E-value=0.047  Score=33.31  Aligned_cols=46  Identities=11%  Similarity=0.146  Sum_probs=38.8

Q ss_pred             EEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE
Q ss_conf             368841797089999974999899999999854015610169988899997
Q gi|254780879|r  277 DLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV  327 (652)
Q Consensus       277 ~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~  327 (652)
                      ..++|++||||+.|.+++|++..++.++    +.+.+. .+..||.|.+..
T Consensus        67 ~~~~V~~gdtL~~Ia~~~~~tv~~l~~~----n~l~~~-~i~~gq~l~~~~  112 (124)
T COG1388          67 VTYTVKKGDTLSKIARKYGVTVAELKQL----NNLSSD-KIKVGQKLKLPV  112 (124)
T ss_pred             CCEEECCCCCHHHHHHHHCCCHHHHHHH----HCCCCC-CCCCCCEEEECC
T ss_conf             6146616875788787708889998765----204576-433475166314


No 23 
>PRK09439 glucose-specific PTS system component; Provisional
Probab=94.52  E-value=0.12  Score=30.40  Aligned_cols=79  Identities=22%  Similarity=0.252  Sum_probs=52.7

Q ss_pred             CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEE-------EECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE
Q ss_conf             43404434642003026796727971596799965-------30897007999839974882002144541188997883
Q gi|254780879|r  504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKAN-------WAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK  576 (652)
Q Consensus       504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag-------~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~  576 (652)
                      .|++-..-|-.|+-+- |.+--|+|.-+|+|...-       -....|--|.| |= |.-|.=.+=..|-.-|++||+|+
T Consensus        39 D~vFa~k~mGdG~AI~-P~~~~v~AP~~G~V~~vf~T~HAigi~~~~G~eiLI-Hi-GiDTV~L~G~gF~~~v~~Gd~Vk  115 (169)
T PRK09439         39 DVVFAEKIVGDGIAIK-PTGNKIVAPVDGTIGKIFETNHAFSIESDSGVELFV-HF-GIDTVELKGEGFKRIAEEGQRVK  115 (169)
T ss_pred             CHHHHCCCCCCEEEEE-CCCCEEECCCCEEEEEECCCCCEEEEECCCCCEEEE-EE-CCCCEECCCCCEEEEEECCCEEC
T ss_conf             7486057824748998-679989918895999977889389999289989999-97-62402338967269992769988


Q ss_pred             CCCEEEEEC
Q ss_conf             495899841
Q gi|254780879|r  577 QGQIIGWIG  585 (652)
Q Consensus       577 qGQvIG~vG  585 (652)
                      +||.+..+-
T Consensus       116 ~G~~L~~~D  124 (169)
T PRK09439        116 VGDPIIEFD  124 (169)
T ss_pred             CCCEEEEEC
T ss_conf             999999986


No 24 
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=94.36  E-value=0.14  Score=29.99  Aligned_cols=77  Identities=18%  Similarity=0.209  Sum_probs=54.3

Q ss_pred             CCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCC--------CEEEEEHHHHHHHHCCCCCCEEE
Q ss_conf             3404434642003026796727971596799965308970079998399--------74882002144541188997883
Q gi|254780879|r  505 PILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGN--------GYVSSYNHQDAIAKNIKAGTAVK  576 (652)
Q Consensus       505 Pilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~--------Gy~T~YaHlS~~a~gV~~G~~V~  576 (652)
                      |++-..-|=.|+-+- |..--|+|.-+|+|...-..   +..+-|+..+        |.-|...+-..|..-|++||+|+
T Consensus        18 ~vFs~~~~G~G~AI~-P~~~~v~AP~~G~V~~v~~T---~HAigi~t~~G~evLiHiGiDTV~L~G~gF~~~v~~Gd~V~   93 (124)
T cd00210          18 EVFASKMMGDGFAIK-PSDGKVVAPVDGTIVQIFPT---KHAIGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVK   93 (124)
T ss_pred             HHHCCCCCCCEEEEE-CCCCEEECCCCEEEEEECCC---CCEEEEEECCCCEEEEEEEECCCCCCCCCEEEEECCCCEEC
T ss_conf             587568822769998-47998990789799998678---96999996899899999730420148953189974889998


Q ss_pred             CCCEEEEEC
Q ss_conf             495899841
Q gi|254780879|r  577 QGQIIGWIG  585 (652)
Q Consensus       577 qGQvIG~vG  585 (652)
                      +||.+..+=
T Consensus        94 ~G~~L~~~D  102 (124)
T cd00210          94 QGDKLLEFD  102 (124)
T ss_pred             CCCEEEEEC
T ss_conf             999999985


No 25 
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family; InterPro: IPR010129   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    Type I secretion is an ABC transporter that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C terminus of the transported protein. This entry represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This entry selects a group of sequences closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.; GO: 0015031 protein transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=94.15  E-value=0.068  Score=32.15  Aligned_cols=24  Identities=21%  Similarity=0.057  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9989899999999999999987626
Q gi|254780879|r   42 WLSTTFFAGITSGVIIGGSLLTALD   66 (652)
Q Consensus        42 w~~~t~ltg~~~~~l~g~a~~~ald   66 (652)
                      ||.--++.++|-+++ +-|.|+-||
T Consensus         5 r~~~~~~~~~v~~~~-~WA~~~~ld   28 (434)
T TIGR01843         5 RLITWLIALLVVIFL-LWAAFAPLD   28 (434)
T ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHC
T ss_conf             988999999999999-988876102


No 26 
>PRK11649 hypothetical protein; Provisional
Probab=94.11  E-value=0.46  Score=26.30  Aligned_cols=59  Identities=14%  Similarity=0.245  Sum_probs=49.3

Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECC
Q ss_conf             77640136884179708999997499989999999985401561016998889999727
Q gi|254780879|r  271 IPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQ  329 (652)
Q Consensus       271 ~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~  329 (652)
                      ..+|.+..+.-.=..+|+..+.++|++..++.+++..|.-..+.+.|+.|+.+.+.++.
T Consensus       158 ~~e~~~~~~~G~I~~Sl~~Sa~~aGl~~~~i~~l~~i~~~~IDFrdlr~GD~F~Vl~e~  216 (418)
T PRK11649        158 QGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSVLMSR  216 (418)
T ss_pred             CCCCCCCEEEEEECCCHHHHHHHCCCCHHHHHHHHHHHCCCCEEEECCCCCEEEEEEEE
T ss_conf             56542224799990608999988599989999999984686110024899879999999


No 27 
>pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1.
Probab=93.69  E-value=0.25  Score=28.13  Aligned_cols=78  Identities=22%  Similarity=0.263  Sum_probs=51.4

Q ss_pred             CCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-------CCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEEC
Q ss_conf             340443464200302679672797159679996530-------8970079998399748820021445411889978834
Q gi|254780879|r  505 PILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-------GGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQ  577 (652)
Q Consensus       505 Pilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-------~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~q  577 (652)
                      |++-..-|=.|+-+- |..--|+|.-+|+|...-..       .-.|--|.| |= |.-|.=.+=..|..-|++||+|++
T Consensus        23 ~vFs~~~~G~G~AI~-P~~~~v~AP~~G~V~~v~~T~HAigi~~~~G~eiLi-Hi-GiDTV~L~G~gF~~~v~~Gd~V~~   99 (133)
T pfam00358        23 QVFASKMMGDGFAIK-PSDGKVVAPVDGTIVQIFPTKHAIGIESDGGVEILI-HV-GIDTVKLNGEGFESHVEEGDRVKQ   99 (133)
T ss_pred             HHHCCCCCCCEEEEE-CCCCEEEECCCEEEEEECCCCCEEEEEECCCCEEEE-EE-CCCCEECCCCCEEEEECCCCEECC
T ss_conf             476568822769998-479979907897999986899799999689989999-98-645223389631899758999989


Q ss_pred             CCEEEEEC
Q ss_conf             95899841
Q gi|254780879|r  578 GQIIGWIG  585 (652)
Q Consensus       578 GQvIG~vG  585 (652)
                      ||.|..+=
T Consensus       100 G~~L~~~D  107 (133)
T pfam00358       100 GDKLLEFD  107 (133)
T ss_pred             CCEEEEEC
T ss_conf             99999985


No 28 
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component; InterPro: IPR001127   The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) ,  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.   The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).    The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.    An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , .     ; GO: 0005351 sugar:hydrogen ion symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane.
Probab=93.65  E-value=0.19  Score=29.04  Aligned_cols=68  Identities=24%  Similarity=0.314  Sum_probs=53.8

Q ss_pred             CCEEECCCCCCCEEECCCC--EEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHH------HHHCCCCCCEEECC
Q ss_conf             2003026796727971596--79996-------530897007999839974882002144------54118899788349
Q gi|254780879|r  514 TGVDWAAPRGTPIVAVGDG--IVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDA------IAKNIKAGTAVKQG  578 (652)
Q Consensus       514 ~GVD~aAp~GTPI~Aag~G--~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~------~a~gV~~G~~V~qG  578 (652)
                      +|+=+ -|..=-++|..||  +|..+       |=.+--|--|.| |= |.-|.=..=..      |-.-|++||+|+||
T Consensus        27 dG~AI-~P~~g~v~AP~dGGv~i~~~F~T~HA~gi~s~~G~EiLi-H~-GIDTV~L~G~GPGELEvF~~~v~~G~~V~~G  103 (129)
T TIGR00830        27 DGFAI-LPTDGEVVAPVDGGVKITKIFPTKHAIGIESDSGVEILI-HI-GIDTVKLNGEGPGELEVFTSHVEEGDKVKKG  103 (129)
T ss_pred             CCEEE-ECCCCCEECCCCCCEEEEEECCCCCEEEEEECCCEEEEE-EC-CCCEEEECCCCCCEEEEEEEEEEECCEECCC
T ss_conf             86787-408981782421652898973898479998289839999-82-4235887874896131247876438787179


Q ss_pred             CEEEEE
Q ss_conf             589984
Q gi|254780879|r  579 QIIGWI  584 (652)
Q Consensus       579 QvIG~v  584 (652)
                      |.|..+
T Consensus       104 d~l~ef  109 (129)
T TIGR00830       104 DPLLEF  109 (129)
T ss_pred             CEEEEE
T ss_conf             779995


No 29 
>PRK09824 beta-glucoside-specific PTS system components IIABC; Provisional
Probab=92.27  E-value=0.6  Score=25.49  Aligned_cols=79  Identities=14%  Similarity=0.169  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE
Q ss_conf             4340443464200302679672797159679996-------530897007999839974882002144541188997883
Q gi|254780879|r  504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK  576 (652)
Q Consensus       504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~  576 (652)
                      +|++-..-|-+|+-+- |.---|+|.-||+|...       |-.+..|--+.| |= |..|.=.+=..|..-|++||+|+
T Consensus       495 D~~Fa~~~~G~g~ai~-p~~g~v~aP~~g~v~~~~~t~HAig~~~~~G~e~li-Hi-GidTV~l~G~~F~~~v~~g~~V~  571 (625)
T PRK09824        495 DTTFASGLLGKGIAIL-PSVGEVRSPVAGRIASLFATLHAIGIESDDGVEILI-HV-GIDTVKLDGKFFSAHVNVGDKVN  571 (625)
T ss_pred             CHHHCCCCCCCCEEEE-CCCCEEECCCCCEEEEECCCCCEEEEECCCCCEEEE-EE-CCCCCCCCCCCCEEEECCCCEEC
T ss_conf             6554036777966995-699969807980898974789678997289818999-96-61650108915416746789967


Q ss_pred             CCCEEEEEC
Q ss_conf             495899841
Q gi|254780879|r  577 QGQIIGWIG  585 (652)
Q Consensus       577 qGQvIG~vG  585 (652)
                      +||.+...-
T Consensus       572 ~g~~l~~~d  580 (625)
T PRK09824        572 TGDRLISFD  580 (625)
T ss_pred             CCCEEEEEC
T ss_conf             999899974


No 30 
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=92.06  E-value=0.13  Score=30.29  Aligned_cols=50  Identities=22%  Similarity=0.254  Sum_probs=38.3

Q ss_pred             EEEEECCCCCHHHHHHHC-CCCHHHHHHHHHHHHC--CCCHHHCCCCCEEEEEE
Q ss_conf             368841797089999974-9998999999998540--15610169988899997
Q gi|254780879|r  277 DLIPIQHNTTIFDAMVHA-GYSNGDSAKIAKALKN--EVRVDQLTKDEILRIGV  327 (652)
Q Consensus       277 ~~v~VK~GDTL~~IL~r~-Gvs~~ei~~i~~al~~--~~~~~~Lr~Gq~L~I~~  327 (652)
                      ..++|++||||+.|.++. |... +-..|..+.+.  ..+.+.|.+||.|+|+-
T Consensus       211 ~~~~v~rgDTl~~is~~~Yg~~~-~y~~I~~aNk~~~~~~pd~I~pGq~l~iP~  263 (269)
T COG1652         211 TTNTVKRGDTLWQISKKVYGDGV-EYRKIAEANKALVLDNPDKIKPGQVLRIPD  263 (269)
T ss_pred             EEEEEECCCCHHHHHHHHCCCCC-EEEHHHHHHCCCCCCCCCCCCCCCEEECCC
T ss_conf             27897038844231286608721-110488761421157835367887764686


No 31 
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=91.82  E-value=0.41  Score=26.67  Aligned_cols=162  Identities=21%  Similarity=0.260  Sum_probs=87.9

Q ss_pred             HCCCCHHHHHCCCCC---EEEEEE-EEECCCCCCCCC--------CCEEEEE--EECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             301110121014454---068875-321157851246--------7236889--62388542013455766554443355
Q gi|254780879|r  411 LASSVNLQEHLKPTD---FLETFF-SVNHANNQASDD--------SELLYIH--ARFGETRTRFYRFLNPVDGSVEYFNE  476 (652)
Q Consensus       411 ~a~dVDFqr~ir~GD---~f~Vly-e~~~~~g~~~~~--------geil~A~--~~~~g~~~~~yrf~~~~~~~~~yyd~  476 (652)
                      |+|=--..|.|+.|+   .-+|.| +...++...+..        +.++...  ....|..   +...  ....++|-|=
T Consensus       658 yGFIETPYr~V~~g~v~~~~~v~YLtA~eEd~~~iAQa~~~lDe~g~i~~d~V~~R~~G~e---~~~~--~~~~VdyMDV  732 (1449)
T TIGR02013       658 YGFIETPYRKVKDGKVVVDDEVDYLTADEEDNYVIAQANAPLDENGRIVEDLVVARYRGDE---ITLV--SPDEVDYMDV  732 (1449)
T ss_pred             CCCCCCCCEEEECCEEEECCCCEECCHHHHCCEEEECCCCCCCCCCCCCCCEEEEEECCCC---CCCC--CCCCEEEEEE
T ss_conf             7751367678745323333641343512236716703544318897052356888654773---2211--6760247651


Q ss_pred             CCCCHHH-------CCCCCCCCCCCCCCCCCCCC--CCCCCCCCCC--CCEE--ECCCCCCCEEECCCCEEEEEEEECCC
Q ss_conf             6610000-------01123334541023567641--4340443464--2003--02679672797159679996530897
Q gi|254780879|r  477 NGKSSRP-------FLLRTPVPFGRMTSGFGMRY--HPILGYSRMH--TGVD--WAAPRGTPIVAVGDGIVEKANWAGGY  543 (652)
Q Consensus       477 ~G~S~~k-------~llr~Pv~~~risS~Fg~R~--hPilg~~r~H--~GVD--~aAp~GTPI~Aag~G~V~~ag~~~Gy  543 (652)
                      +.+..-.       ||-.-=-+.+=|-|  ||-|  -|.|.-=+|=  ||.=  .|.=.|+=|+|=.+|+|.|.     =
T Consensus       733 SP~Q~VSVaAaLIPFLEHDDANRALMGs--NMQRQAVPLL~seaP~VGTGmE~~~A~DSG~~i~A~~~GvV~~V-----d  805 (1449)
T TIGR02013       733 SPKQIVSVAAALIPFLEHDDANRALMGS--NMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRAGVVEYV-----D  805 (1449)
T ss_pred             CCHHHHHHHHHCCCCCCCCHHHHHHHHC--CCHHHCCCCCCCCCCCCCCHHHHHHHHCCCEEEEECCCCEEEEE-----E
T ss_conf             8323556655426332354145665412--53123677787798823202789886235408997069789998-----4


Q ss_pred             CCEEEEECC--------CC-----EEEEEH-------------HHHHHHHCCCCCCEEECCCEEEEECCC
Q ss_conf             007999839--------97-----488200-------------214454118899788349589984166
Q gi|254780879|r  544 GKQTLIHHG--------NG-----YVSSYN-------------HQDAIAKNIKAGTAVKQGQIIGWIGTT  587 (652)
Q Consensus       544 Gn~V~I~H~--------~G-----y~T~Ya-------------HlS~~a~gV~~G~~V~qGQvIG~vGsT  587 (652)
                      ++.|.|+..        +|     +.-.|-             |+--|   |++|++|..|||||===||
T Consensus       806 a~~I~v~~~~~~~~~~~~g~DPd~~~~~Y~L~Ky~RSNQ~TC~nQ~Pi---V~~GDrV~~GdvlADGPsT  872 (1449)
T TIGR02013       806 AKRIVVRYKEKEEEETVSGDDPDAAIDIYRLLKYQRSNQDTCINQRPI---VSVGDRVEAGDVLADGPST  872 (1449)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCEECCEEE---CCCCCEECCCCEEECCCCC
T ss_conf             778899314776665557788322025750467631478840145355---0148681021277347666


No 32 
>PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=91.54  E-value=0.51  Score=26.03  Aligned_cols=31  Identities=16%  Similarity=0.330  Sum_probs=16.1

Q ss_pred             CCCCEEEEEHHHHHHHHCCCCCCEEECCCEE
Q ss_conf             3997488200214454118899788349589
Q gi|254780879|r  551 HGNGYVSSYNHQDAIAKNIKAGTAVKQGQII  581 (652)
Q Consensus       551 H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvI  581 (652)
                      -.+|..|-|.-...-..-|+.|++|.-||-|
T Consensus      1028 e~d~~~~ey~~~~g~~~~v~~g~~V~~ge~l 1058 (1295)
T PRK02597       1028 EDDGTITEYPILPGQNVMVSDGQQVDAGEPL 1058 (1295)
T ss_pred             ECCCCCEECCCCCCCCEEECCCCEEECCCCC
T ss_conf             2267420013455632242257366136524


No 33 
>TIGR02005 PTS-IIBC-alpha PTS system, alpha-glucoside-specific IIBC component; InterPro: IPR010975   This entry represents the fused PTS enzyme II B and C domains. A gene from Clostridium  has been partially characterised as a maltose transporter, while genes from Fusobacterium and Klebsiella ,  have been proposed to transport the five non-standard isomers of sucrose.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system.
Probab=91.24  E-value=0.29  Score=27.78  Aligned_cols=67  Identities=9%  Similarity=0.072  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCC-HHHHHHHHHHHHCCCCHHHCC
Q ss_conf             1122334222665445677776401368841797089999974999-899999999854015610169
Q gi|254780879|r  252 IKIIEENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYS-NGDSAKIAKALKNEVRVDQLT  318 (652)
Q Consensus       252 ~~~~~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs-~~ei~~i~~al~~~~~~~~Lr  318 (652)
                      ..|..-|+..+-.+...++.+-|......-|+||+-+.--.+.+.+ +++++.++++|.+.-|+..+.
T Consensus       409 fLIlkFn~~tpGRe~~eEEvKLYsKadYKak~G~~~e~~~~~~~~~yedkA~~fL~ALGG~~NI~~v~  476 (533)
T TIGR02005       409 FLILKFNIATPGREDEEEEVKLYSKADYKAKKGESKESKEAELESEYEDKAAAFLQALGGKENIKDVT  476 (533)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             99877078975688754432212103455127875210150015786899999996368874302344


No 34 
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component; InterPro: IPR011297   The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) ,  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.   The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).    The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.    An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , .    This entry represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (hydroquinone-O-beta-D-glucopyranoside) . These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system.
Probab=91.00  E-value=0.46  Score=26.33  Aligned_cols=68  Identities=28%  Similarity=0.315  Sum_probs=52.7

Q ss_pred             CCEEECCCCCCCEEECCCCEEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE
Q ss_conf             200302679672797159679996-------53089700799983997488200214454118899788349589984
Q gi|254780879|r  514 TGVDWAAPRGTPIVAVGDGIVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI  584 (652)
Q Consensus       514 ~GVD~aAp~GTPI~Aag~G~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v  584 (652)
                      +||=+ -|..+-|+|.-||+|+-.       |=.+-.|==|.| |= |.-|.=..=.-|--.|++|++|++||..+.+
T Consensus       538 ~G~Ai-~P~eG~~~AP~dG~v~~VF~T~HAiGi~~~nG~E~LI-Hv-GIDTV~L~G~~Fe~~V~~Gd~v~~Gq~L~~~  612 (660)
T TIGR01995       538 KGVAI-LPSEGEVVAPVDGTVTAVFPTKHAIGIRSDNGVEILI-HV-GIDTVELKGEYFEILVKVGDKVKAGQLLLTF  612 (660)
T ss_pred             CCEEE-EECCCEEECCCCCEEEEEECCCCEEEECCCCCEEEEE-EE-EEEEEEECCEEEEEEEEECCEEEECCCCCEE
T ss_conf             84589-7158778823377899997486227412689728999-84-1234565450122214566787506631221


No 35 
>PRK10255 N-acetyl glucosamine specific PTS system components IIABC; Provisional
Probab=90.54  E-value=1.2  Score=23.35  Aligned_cols=85  Identities=18%  Similarity=0.200  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-------CCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE
Q ss_conf             4340443464200302679672797159679996530-------897007999839974882002144541188997883
Q gi|254780879|r  504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-------GGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK  576 (652)
Q Consensus       504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-------~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~  576 (652)
                      +|++-..-|-+|+-+- |..--|+|.-||+|+..=..       .--|--|.| |= |..|+=..=..|-.-|++||+|+
T Consensus       517 D~vFa~~~mG~G~aI~-P~~g~v~aP~dG~i~~vf~T~HA~gi~~~~G~EiLi-Hi-GiDTV~L~G~gF~~~v~~Gd~Vk  593 (648)
T PRK10255        517 DEAFASKAVGDGVAVK-PTDKIVVSPAAGTIVKIFNTNHAFCLETEKGAEIVV-HM-GIDTVALEGKGFKRLVEEGAQVS  593 (648)
T ss_pred             CHHHHHCCCCCCEEEE-CCCCEEECCCCCEEEEECCCCCEEEEECCCCCEEEE-EE-EECCEEECCCCCEEEECCCCEEC
T ss_conf             7555314557856994-589959806885799971688579998489818999-95-44524217805348834859967


Q ss_pred             CCCEEEEEC-----CCCCCC
Q ss_conf             495899841-----667888
Q gi|254780879|r  577 QGQIIGWIG-----TTGLST  591 (652)
Q Consensus       577 qGQvIG~vG-----sTG~ST  591 (652)
                      +||.+..+-     .-|+++
T Consensus       594 ~G~~l~~~D~~~i~~~g~~~  613 (648)
T PRK10255        594 AGQPILEMDLDYLNANARSM  613 (648)
T ss_pred             CCCEEEEECHHHHHHCCCCC
T ss_conf             99988997499998509998


No 36 
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=90.43  E-value=1.2  Score=23.51  Aligned_cols=78  Identities=24%  Similarity=0.275  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCEEECCCCCCCEEECCCCEEEEE-------EEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEEC
Q ss_conf             340443464200302679672797159679996-------5308970079998399748820021445411889978834
Q gi|254780879|r  505 PILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKA-------NWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQ  577 (652)
Q Consensus       505 Pilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~a-------g~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~q  577 (652)
                      |++-...|-.|+-+- |..--|+|..||+|...       |-..--|--+.| |= |.-|.=..=..|-.-|++|++|++
T Consensus        25 ~vFs~k~mGdGiAI~-P~~g~vvAPvdG~v~~iFpTkHAigi~t~~GvEiLi-Hi-GiDTV~L~GegF~~~v~~Gd~Vk~  101 (156)
T COG2190          25 PVFSEKMVGDGVAIK-PSEGEVVAPVDGTVVLIFPTKHAIGIETDEGVEILI-HI-GIDTVKLNGEGFESLVKEGDKVKA  101 (156)
T ss_pred             HHHHCCCCCCCEEEE-CCCCEEEECCCCEEEEEEECCCEEEEECCCCCEEEE-EE-CEEEEEECCCCEEEEEECCCEECC
T ss_conf             676415634867994-689959812685899985178479998389959999-95-640586889324787507998815


Q ss_pred             CCEEEEEC
Q ss_conf             95899841
Q gi|254780879|r  578 GQIIGWIG  585 (652)
Q Consensus       578 GQvIG~vG  585 (652)
                      ||.+..+-
T Consensus       102 Gd~Li~fD  109 (156)
T COG2190         102 GDPLLEFD  109 (156)
T ss_pred             CCEEEEEC
T ss_conf             98989997


No 37 
>PRK05305 phosphatidylserine decarboxylase; Provisional
Probab=89.53  E-value=1.4  Score=22.86  Aligned_cols=19  Identities=21%  Similarity=0.475  Sum_probs=15.8

Q ss_pred             HCCCCCCEEECCCEEEEEC
Q ss_conf             1188997883495899841
Q gi|254780879|r  567 KNIKAGTAVKQGQIIGWIG  585 (652)
Q Consensus       567 ~gV~~G~~V~qGQvIG~vG  585 (652)
                      -.+++|++|+|||-||...
T Consensus       160 ~~~~~g~~l~~G~r~G~I~  178 (214)
T PRK05305        160 CYVEEGDELERGERFGLIR  178 (214)
T ss_pred             ECCCCCCEEECCCEEEEEE
T ss_conf             2267897885377773796


No 38 
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=89.21  E-value=1.6  Score=22.50  Aligned_cols=44  Identities=11%  Similarity=0.155  Sum_probs=24.3

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEE
Q ss_conf             96799965308970079998399748820021445411889978834958998
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGW  583 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~  583 (652)
                      +|.|+..     ..+.++||.+.-|.-.  .=+-+.  +.-|+-|++|+.++.
T Consensus      1080 SGQIi~I-----~~~~ivIR~akPYLaS--~GA~vh--~~~GdlI~eGDtLvT 1123 (1350)
T CHL00117       1080 SGQILII-----QVDSIVIRSAKPYLAT--PGATVH--GHYGEILYEGDTLVT 1123 (1350)
T ss_pred             CCCEEEE-----ECCEEEEEECCCEECC--CCCEEE--CCCCCEECCCCEEEE
T ss_conf             7228998-----4787999943631259--997897--048988679987899


No 39 
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=88.86  E-value=1.2  Score=23.46  Aligned_cols=21  Identities=38%  Similarity=0.661  Sum_probs=13.7

Q ss_pred             CCCEEECCCCCCCE-------EECCCCE
Q ss_conf             42003026796727-------9715967
Q gi|254780879|r  513 HTGVDWAAPRGTPI-------VAVGDGI  533 (652)
Q Consensus       513 H~GVD~aAp~GTPI-------~Aag~G~  533 (652)
                      ..||-|..|.|--|       +|.+.|.
T Consensus       294 ~Lg~tf~~P~Gf~IdN~~~Avlatg~ge  321 (479)
T COG4784         294 ELGVTFDVPDGFKIDNSAEAVLATGPGE  321 (479)
T ss_pred             CCCEEEECCCCEEECCCHHHHHCCCCCC
T ss_conf             6653885688637637468762458863


No 40 
>pfam01333 Apocytochr_F_C Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034.
Probab=87.86  E-value=1.3  Score=23.03  Aligned_cols=83  Identities=16%  Similarity=0.114  Sum_probs=52.5

Q ss_pred             CCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECC
Q ss_conf             72797159679996530897007999839974882002144541188997883495899841667888742688997867
Q gi|254780879|r  524 TPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNG  603 (652)
Q Consensus       524 TPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG  603 (652)
                      +..-|...|+|........-|..|.|...+|-.+.-.--..----|++|+.|+.||-+-.==+-|---  ...-||.   
T Consensus         3 nv~~as~~G~I~~I~~~ekg~~~vtI~t~dG~~v~~~IP~GpeliV~~G~~V~~dqpLT~nPNVGGFG--Q~etEIV---   77 (118)
T pfam01333         3 NVYNASAAGTITKITRNEKGGYEVTIETADGETVVETIPAGPELIVSEGQTVKADQPLTNNPNVGGFG--QAETEIV---   77 (118)
T ss_pred             CEEECCCCEEEEEEEECCCCCEEEEEECCCCCEEEEECCCCCEEEECCCCEEECCCCCCCCCCCCCCC--CCCEEEE---
T ss_conf             54716677089997756788579999869998998853999748973898886698444599856657--6505999---


Q ss_pred             EECCCCEEC
Q ss_conf             883662000
Q gi|254780879|r  604 IKVDSTKVR  612 (652)
Q Consensus       604 ~~VdP~~~~  612 (652)
                       -.||.|++
T Consensus        78 -LQ~P~Rv~   85 (118)
T pfam01333        78 -LQNPNRVQ   85 (118)
T ss_pred             -ECCHHHHH
T ss_conf             -51825845


No 41 
>TIGR03309 matur_yqeB selenium-dependent molybdenum hydroxylase system protein, YqeB family. Members of this protein family are probable accessory proteins for the biosynthesis of enzymes with labile selenium-containing centers, different from selenocysteine-containing proteins.
Probab=87.41  E-value=0.8  Score=24.61  Aligned_cols=19  Identities=32%  Similarity=0.594  Sum_probs=13.7

Q ss_pred             CCCCCEEECCCEEEEECCC
Q ss_conf             8899788349589984166
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGTT  587 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGsT  587 (652)
                      .+-|+.|++||+||++|.+
T Consensus       179 ~~IGd~V~kG~vig~v~~~  197 (256)
T TIGR03309       179 KAIGDSVKKGDVIATVGDV  197 (256)
T ss_pred             HHCCCEEECCCEEEEECCE
T ss_conf             4418968679689998998


No 42 
>TIGR02971 heterocyst_DevB ABC exporter membrane fusion protein, DevB family; InterPro: IPR014315   Members of this protein are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. (strain PCC 7120) is partially characterised as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. which has seven members..
Probab=87.10  E-value=0.55  Score=25.78  Aligned_cols=18  Identities=17%  Similarity=0.158  Sum_probs=9.4

Q ss_pred             HCCCCHHH----CCCCCEEEEE
Q ss_conf             40156101----6998889999
Q gi|254780879|r  309 KNEVRVDQ----LTKDEILRIG  326 (652)
Q Consensus       309 ~~~~~~~~----Lr~Gq~L~I~  326 (652)
                      -++.=++.    ...|+.|+|.
T Consensus       225 le~t~~~aRLvaP~~G~vLKi~  246 (363)
T TIGR02971       225 LELTYVKARLVAPIDGRVLKIH  246 (363)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEC
T ss_conf             8767677763078987688755


No 43 
>CHL00006 consensus
Probab=86.57  E-value=1.3  Score=23.09  Aligned_cols=57  Identities=19%  Similarity=0.209  Sum_probs=27.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             3356657788998534765445788541131899989899999999999999987626884100
Q gi|254780879|r    9 KRDILFSFGDTPPILGNNDAKIFLDNRRKVSLRWLSTTFFAGITSGVIIGGSLLTALDGHQKIA   72 (652)
Q Consensus         9 ~~~~~~~~g~eppl~~~~~~~~~~~~rr~vs~rw~~~t~ltg~~~~~l~g~a~~~aldg~~~~a   72 (652)
                      ..+-+++||+-=-+.+.-+  ..-| --|..+|    ||-||-.=+.=+.--+.|..+|--.|-
T Consensus       307 ~~~~~v~~geavgiiaaqs--igep-gtqlt~r----tfhtggvf~~~~~~~~~~~~~g~i~f~  363 (1372)
T CHL00006        307 THGDLVELGEAVGIIAGQS--IGEP-GTQLTLR----TFHTGGVFTGGTAEHVRAPSNGKIKFN  363 (1372)
T ss_pred             CCCCCCCCCCEEEEEEEEC--CCCC-CCCCEEE----EEECCCCCCCCCHHHCCCCCCCEEECC
T ss_conf             2687355575334774201--5887-6431244----210165213420110127767447526


No 44 
>PRK05258 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=85.22  E-value=2.6  Score=20.98  Aligned_cols=72  Identities=18%  Similarity=0.315  Sum_probs=47.7

Q ss_pred             CCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEE--HHHHHHHHCCCCCCEEECCCEE
Q ss_conf             4434642003026796727971596799965308970079998399748820--0214454118899788349589
Q gi|254780879|r  508 GYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSY--NHQDAIAKNIKAGTAVKQGQII  581 (652)
Q Consensus       508 g~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~Y--aHlS~~a~gV~~G~~V~qGQvI  581 (652)
                      |.-|.-.=++-.-|.|++|.+.-+|+|.+.....+....+++.....-.-.|  .+..++.  |+.|+.|.+||.+
T Consensus       952 GvPRl~EifeAr~pk~~aiisei~g~v~~i~~~~~~~~~~i~~~~~~~~~~y~ip~~~~l~--v~~gd~V~~G~~l 1025 (1204)
T PRK05258        952 GLPRVQELFEARNPKGQAVITEVDGTVVAIEEDKADRTKEVTVKGETETRSYTIPYTARLK--VEEGDEVERGDEL 1025 (1204)
T ss_pred             CCCCHHHHHHCCCCCCCCEEEEECCEEEEEEECCCCEEEEEEECCCCEEEEEECCCCCEEE--EECCCEEECCCCC
T ss_conf             7602899985047788612675145688745426741799997799648999805775687--7059998448762


No 45 
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=84.27  E-value=2  Score=21.83  Aligned_cols=66  Identities=20%  Similarity=0.199  Sum_probs=46.4

Q ss_pred             CEEECCCCC--CCEEECCCCEEEEEEEECCCCCEEEEECCC---CEEEEEHHHHHHHHCCCCCCEEECCCEE
Q ss_conf             003026796--727971596799965308970079998399---7488200214454118899788349589
Q gi|254780879|r  515 GVDWAAPRG--TPIVAVGDGIVEKANWAGGYGKQTLIHHGN---GYVSSYNHQDAIAKNIKAGTAVKQGQII  581 (652)
Q Consensus       515 GVD~aAp~G--TPI~Aag~G~V~~ag~~~GyGn~V~I~H~~---Gy~T~YaHlS~~a~gV~~G~~V~qGQvI  581 (652)
                      =.|=..|.|  --++|=-||+|.+.+..---.+.|.|+-++   .+.+.+=-+.+=. -|+.|++|+.||.|
T Consensus      1324 LFEar~PK~~e~A~Iae~dG~v~~~~~~~k~~r~~~i~~e~~~~e~~~Y~Ip~~~~L-~V~~G~~V~~G~~l 1394 (1552)
T TIGR02386      1324 LFEARTPKDFEAAVIAEVDGVVEIIEDDVKNKRVVVIKDENDDGEEKEYLIPFGAQL-RVKDGDSVSAGDKL 1394 (1552)
T ss_pred             HHHCCCCCCCCCCCEEHCCCEEEEECCCCCCEEEEEEECCCCCCCEEEEEEECCCEE-EEECCCEEECCCEE
T ss_conf             860168861121100010217885114423408999831688853478765066658-97218887078520


No 46 
>PRK09603 DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=84.24  E-value=2.9  Score=20.67  Aligned_cols=108  Identities=21%  Similarity=0.316  Sum_probs=61.1

Q ss_pred             CCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHH-HHHHHCCCCCCEEECCCEEEEECCCCCCCCCE-----
Q ss_conf             796727971596799965308970079998399748820021-44541188997883495899841667888742-----
Q gi|254780879|r  521 PRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQ-DAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPH-----  594 (652)
Q Consensus       521 p~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHl-S~~a~gV~~G~~V~qGQvIG~vGsTG~STGPH-----  594 (652)
                      |.-.-|.|--+|+|.+.....|--.. +|...+|-.+.|.=- ++. --|..|+.|+.||.+-    .|. --||     
T Consensus      2661 PK~~ailae~~G~V~~g~~~~~~~~i-ii~~~dg~~~ey~i~~g~~-l~V~~Gd~V~~Ge~Lt----dG~-inphdIL~i 2733 (2890)
T PRK09603       2661 PKDVAILSEVDGIVSFGKPIRNKEHI-IVTSKDGRSMDYFVDKGKQ-ILVHADEFVHAGEAMT----DGV-VSSHDILRI 2733 (2890)
T ss_pred             CCCCEEEECCCCEEEECCCCCCCEEE-EEECCCCCEEEEECCCCCE-EEECCCCEEECCCCCC----CCC-CCHHHHHHH
T ss_conf             88743895365189956534785269-9976999477775489987-7767998870688823----799-998999984


Q ss_pred             ---------------------------EEEEEEECCEECCCCEECCCC-CCCCCHHH--HHHHHHHHHHHHH
Q ss_conf             ---------------------------688997867883662000788-78788899--9999999999999
Q gi|254780879|r  595 ---------------------------LHYELIVNGIKVDSTKVRIPE-RENLKGDL--LQRFAMEKKRINS  636 (652)
Q Consensus       595 ---------------------------LHfEv~vnG~~VdP~~~~lp~-~~~l~~~~--l~~F~~~~~~id~  636 (652)
                                                 =|.||+|.- -..=.+|.-|. ..-|+|+.  +..|+.+-+++..
T Consensus      2734 ~g~~~lq~yLVnEVQ~VYrsQGV~InDKHIEVIVRQ-MtsKV~I~d~GDT~fLpGElV~~~~~e~~N~~~~~ 2804 (2890)
T PRK09603       2734 SGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQ-MLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIA 2804 (2890)
T ss_pred             HCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEE-CCCEEEEECCCCCCCCCCCEEEHHHHHHHHHHHHH
T ss_conf             079999999999999999966985536278998751-37469995688888788567629999999999997


No 47 
>pfam02666 PS_Dcarbxylase Phosphatidylserine decarboxylase. This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyse the reaction: Phosphatidyl-L-serine <= phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine.
Probab=83.78  E-value=3  Score=20.54  Aligned_cols=17  Identities=29%  Similarity=0.626  Sum_probs=9.7

Q ss_pred             CCCCEEECCCEEEEECC
Q ss_conf             89978834958998416
Q gi|254780879|r  570 KAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       570 ~~G~~V~qGQvIG~vGs  586 (652)
                      ++|+.|++||-||+---
T Consensus       153 ~~g~~v~kG~e~G~f~f  169 (201)
T pfam02666       153 EEGDEVKKGDELGYFKF  169 (201)
T ss_pred             CCCCEEECCCEEEEEEC
T ss_conf             58979845748807962


No 48 
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=83.49  E-value=1.7  Score=22.37  Aligned_cols=54  Identities=28%  Similarity=0.509  Sum_probs=34.0

Q ss_pred             CCCCCEEECCCCEEEEEEEECCCCCEEEEECCCC------EEEEEH-------------HHHHHHHCCCCCCEEECCCEE
Q ss_conf             7967279715967999653089700799983997------488200-------------214454118899788349589
Q gi|254780879|r  521 PRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNG------YVSSYN-------------HQDAIAKNIKAGTAVKQGQII  581 (652)
Q Consensus       521 p~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~G------y~T~Ya-------------HlS~~a~gV~~G~~V~qGQvI  581 (652)
                      -.|+-|.|-.+|+|.|..     ++.|.|+..+.      ..-.|-             |+-   +-|+.|++|+.||+|
T Consensus       647 ds~~~~~a~~~G~v~yvd-----~~~I~i~~~~~~~~~~~~~~~y~l~~y~~sNq~T~~~Q~---PlV~~~~~v~~~~~i  718 (1127)
T PRK00405        647 DSGAVVVAKRDGVVEYVD-----ASRIVVRVNDDLAGDEGGVDIYNLTKFTRSNQNTCINQR---PIVKVGDRVEKGDVL  718 (1127)
T ss_pred             HHCCEEEECCCCEEEEEE-----CCEEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCEE---EEEECCCEEECCCEE
T ss_conf             417047854795599974-----788999826545677776379961313666667535640---377339888338781


Q ss_pred             E
Q ss_conf             9
Q gi|254780879|r  582 G  582 (652)
Q Consensus       582 G  582 (652)
                      +
T Consensus       719 a  719 (1127)
T PRK00405        719 A  719 (1127)
T ss_pred             C
T ss_conf             4


No 49 
>PRK06302 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=83.15  E-value=0.82  Score=24.55  Aligned_cols=21  Identities=29%  Similarity=0.517  Sum_probs=13.6

Q ss_pred             CCCCCEEECCCEEEEECCCCC
Q ss_conf             889978834958998416678
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGTTGL  589 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGsTG~  589 (652)
                      |++|++|+.||+|+++=.=.+
T Consensus       102 V~vGd~V~~Gq~v~iIEaMK~  122 (155)
T PRK06302        102 VEVGDTVKEGQTLCIIEAMKM  122 (155)
T ss_pred             CCCCCEECCCCEEEEEEECCC
T ss_conf             246867248988999984243


No 50 
>PRK10260 hypothetical protein; Provisional
Probab=82.81  E-value=3.3  Score=20.28  Aligned_cols=47  Identities=13%  Similarity=0.031  Sum_probs=38.2

Q ss_pred             EEEEECCCCC--HHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE
Q ss_conf             3688417970--89999974999899999999854015610169988899997
Q gi|254780879|r  277 DLIPIQHNTT--IFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV  327 (652)
Q Consensus       277 ~~v~VK~GDT--L~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~  327 (652)
                      ..++++.|||  |.+|+++|++...++.++    |...+.---.+|.++.|+.
T Consensus        41 ~~~~v~~~dt~~L~diAr~y~lG~~ei~~A----NP~vDp~lP~~G~~l~iP~   89 (306)
T PRK10260         41 QVITIPEGNTQPLEYFAAEYQMGLSNMMEA----NPGVDTFLPKGGTVLNIPQ   89 (306)
T ss_pred             EEEEECCCCCHHHHHHHHHHCCCHHHHHHH----CCCCCCCCCCCCCEEEECC
T ss_conf             699947897223999999858058999986----8899986699998898146


No 51 
>COG0511 AccB Biotin carboxyl carrier protein [Lipid metabolism]
Probab=80.23  E-value=2.4  Score=21.32  Aligned_cols=57  Identities=26%  Similarity=0.278  Sum_probs=35.0

Q ss_pred             CCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCC-----CCCCCCEEE
Q ss_conf             967279715967999653089700799983997488200214454118899788349589984166-----788874268
Q gi|254780879|r  522 RGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTT-----GLSTGPHLH  596 (652)
Q Consensus       522 ~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsT-----G~STGPHLH  596 (652)
                      .++.|.|.--|+|.+                            +  -|++|++|+.||++..+=.=     =-|...-.=
T Consensus        69 ~~~~V~SPm~Gtv~~----------------------------~--~V~vGd~V~~Gq~l~IiEAMKmeneI~A~~~G~V  118 (140)
T COG0511          69 GGTQVTSPMVGTVYK----------------------------P--FVEVGDTVKAGQTLAIIEAMKMENEIEAPADGVV  118 (140)
T ss_pred             CCCEEECCCCEEEEE----------------------------E--EECCCCEECCCCEEEEEEEEECCCEECCCCCCEE
T ss_conf             786674787618999----------------------------8--7657999758999999982001553228999689


Q ss_pred             EEEE-ECCEECCC
Q ss_conf             8997-86788366
Q gi|254780879|r  597 YELI-VNGIKVDS  608 (652)
Q Consensus       597 fEv~-vnG~~VdP  608 (652)
                      =||+ .||.+|++
T Consensus       119 ~~Ilv~~G~~Ve~  131 (140)
T COG0511         119 KEILVKNGDPVEY  131 (140)
T ss_pred             EEEEECCCCCCCC
T ss_conf             9999448985268


No 52 
>PRK02693 apocytochrome f; Reviewed
Probab=78.83  E-value=4.5  Score=19.38  Aligned_cols=81  Identities=17%  Similarity=0.167  Sum_probs=53.6

Q ss_pred             CCCEEECCCCEEEEEEEECCCCCEEEEECCCCE---EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEE
Q ss_conf             672797159679996530897007999839974---88200214454118899788349589984166788874268899
Q gi|254780879|r  523 GTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGY---VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYEL  599 (652)
Q Consensus       523 GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy---~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv  599 (652)
                      -|..-|...|+|........-|..|.|...+|-   +|.-+-..-+   |++|+.|+.||-+-.==+-|---  +..-||
T Consensus       196 N~~~~as~~G~I~~I~~~e~G~~~v~I~t~~G~~v~~~iP~Gp~li---V~~G~~v~~~qpLT~nPNVGGFG--Q~d~EI  270 (312)
T PRK02693        196 NNVFTASAAGTITSIETGEDGSYVVTITTEDGEVVTETIPAGPELI---VKEGDAVEAGAPLTNDPNVGGFG--QLDTEI  270 (312)
T ss_pred             CCEECCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEECCCCCEEE---ECCCCEEECCCCCCCCCCCCCCC--CCCEEE
T ss_conf             7255366772788877668886799998899999988529998589---72798885698666799877667--672389


Q ss_pred             EECCEECCCCEEC
Q ss_conf             7867883662000
Q gi|254780879|r  600 IVNGIKVDSTKVR  612 (652)
Q Consensus       600 ~vnG~~VdP~~~~  612 (652)
                      .    -.||.||+
T Consensus       271 V----LQ~P~Ri~  279 (312)
T PRK02693        271 V----LQSPVRVK  279 (312)
T ss_pred             E----ECCHHHHH
T ss_conf             9----22857979


No 53 
>CHL00001 rpoB RNA polymerase beta subunit
Probab=77.72  E-value=4.8  Score=19.16  Aligned_cols=57  Identities=23%  Similarity=0.290  Sum_probs=34.5

Q ss_pred             CCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEE-------------HHHHHHHHCCCCCCEEECCCEEEE
Q ss_conf             26796727971596799965308970079998399748820-------------021445411889978834958998
Q gi|254780879|r  519 AAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSY-------------NHQDAIAKNIKAGTAVKQGQIIGW  583 (652)
Q Consensus       519 aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~Y-------------aHlS~~a~gV~~G~~V~qGQvIG~  583 (652)
                      |--.|+.|.|-.+|.|.|..-     +.|.|....+-.-.|             .|+.   +-|+.|++|+.||+|+.
T Consensus       566 a~ds~~~~~a~~~G~v~y~d~-----~~i~~~~~~~~~~~y~l~~~~rsn~~t~~~q~---P~V~~g~~v~~g~ilad  635 (1065)
T CHL00001        566 ALDSGVVAIAEHEGKIIYVDA-----DKIILSGNKGDTLSIPLVKYQRSNQNTCMHQK---PIVWRGECIKKGQILAD  635 (1065)
T ss_pred             HHCCCCEEEECCCCEEEEEEC-----CEEEEECCCCCEEEEEECCCCCCCCCCCCCCC---EEEECCCEEECCCEECC
T ss_conf             320473688426862888507-----66899637885578752566668755542512---05624867712837435


No 54 
>PRK09890 cold shock protein CspG; Provisional
Probab=76.78  E-value=3  Score=20.62  Aligned_cols=47  Identities=21%  Similarity=0.332  Sum_probs=31.7

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCC-CEEECCCEEEE
Q ss_conf             967999653089700799983997488200214454118899-78834958998
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAG-TAVKQGQIIGW  583 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G-~~V~qGQvIG~  583 (652)
                      .|+|..-.-.+|||-.   ...+|=.-.|-|.|.+.   ..| .....||.|-|
T Consensus         6 tG~VKwFn~~KGyGFI---~~ddg~~DvFvH~s~i~---~~~~~~L~~Gq~V~f   53 (70)
T PRK09890          6 TGLVKWFNADKGFGFI---TPDDGSKDVFVHFTAIQ---SNEFRTLNENQKVEF   53 (70)
T ss_pred             EEEEEEECCCCCEEEE---CCCCCCCCEEEEHHHHC---CCCCCCCCCCCEEEE
T ss_conf             6999988399986997---03899942999868927---268833299999999


No 55 
>cd06254 M14_ASTE_ASPA_like_4 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=76.08  E-value=2.1  Score=21.70  Aligned_cols=19  Identities=32%  Similarity=0.770  Sum_probs=16.9

Q ss_pred             CCCCCCEEECCCEEEEECC
Q ss_conf             1889978834958998416
Q gi|254780879|r  568 NIKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       568 gV~~G~~V~qGQvIG~vGs  586 (652)
                      .++.|++|++||+||++=+
T Consensus       237 ~v~~G~~V~~Gq~lg~I~d  255 (288)
T cd06254         237 FVKAGDTVQKGALLGYVTD  255 (288)
T ss_pred             ECCCCCEECCCCEEEEEEC
T ss_conf             3688999768999999968


No 56 
>PRK10190 hypothetical protein; Provisional
Probab=75.33  E-value=5.5  Score=18.72  Aligned_cols=47  Identities=11%  Similarity=0.005  Sum_probs=37.3

Q ss_pred             EEEEECCCCC--HHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE
Q ss_conf             3688417970--89999974999899999999854015610169988899997
Q gi|254780879|r  277 DLIPIQHNTT--IFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV  327 (652)
Q Consensus       277 ~~v~VK~GDT--L~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~  327 (652)
                      ..++|.++||  |.+|+++|++...++.++    |.-.+.---++|.++.|+.
T Consensus        38 ~~~~v~~~~~~~L~~iAr~y~~G~~~i~~A----NPgvDp~lP~~G~~l~iP~   86 (310)
T PRK10190         38 LTVTVPDHNTQPLETFAAQYGQGLSNMLEA----NPGADVFLPKSGSQLTIPQ   86 (310)
T ss_pred             EEEEECCCCCCCHHHHHHHHCHHHHHHHHH----CCCCCCCCCCCCCEEEECC
T ss_conf             799937898732999999867669999986----8899987799998898066


No 57 
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=75.12  E-value=3.2  Score=20.39  Aligned_cols=39  Identities=23%  Similarity=0.416  Sum_probs=23.4

Q ss_pred             CEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHH---CCCCCCEE
Q ss_conf             679996530897007999839974882002144541---18899788
Q gi|254780879|r  532 GIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAK---NIKAGTAV  575 (652)
Q Consensus       532 G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~---gV~~G~~V  575 (652)
                      |+|..-  +.|||-..-   .+|=...|-|+|.|..   .++.||+|
T Consensus         2 G~Vk~f--~kGfGFI~~---~~g~~DvFvH~s~i~~~~~~l~~Gd~V   43 (64)
T smart00357        2 GVVKWF--NKGFGFIRP---DDGGKDVFVHPSQIQGGLKSLREGDEV   43 (64)
T ss_pred             CEEEEE--ECCEEEEEE---CCCCCCEEEEHHHHCCCCCCCCCCCEE
T ss_conf             479698--284488861---899940999869954677744758789


No 58 
>pfam00313 CSD 'Cold-shock' DNA-binding domain.
Probab=74.77  E-value=4.5  Score=19.38  Aligned_cols=49  Identities=24%  Similarity=0.319  Sum_probs=32.6

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE
Q ss_conf             967999653089700799983997488200214454118899788349589984
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI  584 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v  584 (652)
                      .|+|..-.-..|||-   |.-.+|-.-.|.|.|.+..  .....+++||.+-|-
T Consensus         2 tG~VK~f~~~kGfGF---I~~~~~~~DiFvH~s~l~~--~~~~~L~~G~~V~f~   50 (66)
T pfam00313         2 TGTVKWFNAKKGFGF---ITPEDGDKDVFVHFSAIQG--DGFRSLQEGQRVEFD   50 (66)
T ss_pred             CEEEEEEECCCCEEE---EEECCCCCEEEEEHHHHCC--CCCCCCCCCCEEEEE
T ss_conf             489999959999699---9978998469999268121--478617999999999


No 59 
>TIGR02644 Y_phosphoryl pyrimidine-nucleoside phosphorylase; InterPro: IPR000053   Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, 2.4.2.4 from EC) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, 2.4.2.2 from EC). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin . Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge , . Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference , which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity.; GO: 0006206 pyrimidine base metabolic process.
Probab=74.70  E-value=4.6  Score=19.29  Aligned_cols=57  Identities=25%  Similarity=0.281  Sum_probs=45.7

Q ss_pred             CCCCCCEEECCCCEEEEE--------EEECCCCCEE---EEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC
Q ss_conf             679672797159679996--------5308970079---998399748820021445411889978834958998416
Q gi|254780879|r  520 APRGTPIVAVGDGIVEKA--------NWAGGYGKQT---LIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       520 Ap~GTPI~Aag~G~V~~a--------g~~~GyGn~V---~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs  586 (652)
                      ++.=.+|+|--||.|.+.        +|.=|-|+.-   .|+|.-|..-          ..+.|++|+.||+|.++=+
T Consensus       338 ~k~~~~v~A~~~G~i~~~~a~~~G~a~~~LGAGR~~k~D~ID~~aGi~l----------~~k~Gd~V~~Gd~~~tlY~  405 (425)
T TIGR02644       338 AKYKEEVKAEKSGYISEIDAEELGLAAVDLGAGRARKEDKIDHEAGIYL----------HKKVGDKVKKGDPIATLYS  405 (425)
T ss_pred             CCCEEEEECCCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE----------ECCCCCEEECCCEEEEEEC
T ss_conf             8620233015661365107889989998615887698963001135567----------6566875323757999862


No 60 
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=74.60  E-value=2.5  Score=21.11  Aligned_cols=14  Identities=7%  Similarity=-0.097  Sum_probs=6.0

Q ss_pred             HHHHHHHHCCCCHH
Q ss_conf             25666887199989
Q gi|254780879|r  389 GIWRATSFNGMNSN  402 (652)
Q Consensus       389 SLy~aa~~~gip~~  402 (652)
                      +++.+|....+-.+
T Consensus       327 ~l~~tA~~L~IHrN  340 (376)
T COG3835         327 QLNATAEALFIHRN  340 (376)
T ss_pred             CHHHHHHHHCCCHH
T ss_conf             99899998451051


No 61 
>PRK07051 hypothetical protein; Validated
Probab=73.27  E-value=2.6  Score=21.00  Aligned_cols=18  Identities=22%  Similarity=0.673  Sum_probs=12.3

Q ss_pred             CCCCCEEECCCEEEEECC
Q ss_conf             889978834958998416
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGs  586 (652)
                      |++|++|+.||+|+.+=+
T Consensus        26 V~~Gd~V~~G~~v~iiEa   43 (80)
T PRK07051         26 VEVGDTVAAGDVVGLVEV   43 (80)
T ss_pred             CCCCCEECCCCEEEEEEE
T ss_conf             367999889999999970


No 62 
>PRK10354 major cold shock protein; Provisional
Probab=73.12  E-value=5.2  Score=18.93  Aligned_cols=33  Identities=33%  Similarity=0.410  Sum_probs=25.3

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH
Q ss_conf             967999653089700799983997488200214454
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA  566 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a  566 (652)
                      .|+|.+-.-.+|||-..   -.+|=.-.|-|.|.+.
T Consensus         6 tG~VKwFn~~KGyGFI~---~d~g~~DvFvH~s~l~   38 (70)
T PRK10354          6 TGIVKWFNADKGFGFIT---PDDGSKDVFVHFSAIQ   38 (70)
T ss_pred             EEEEEEEECCCCEEEEE---CCCCCCEEEEEHHHHC
T ss_conf             79999870999859984---2799842999858917


No 63 
>cd06250 M14_PaAOTO_like An uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the the M14 family of metallocarboxypeptidases. This subgroup includes Pseudomonas aeruginosa AotO and related proteins. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. The gene encoding 
Probab=72.65  E-value=3.2  Score=20.42  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=22.1

Q ss_pred             EEEEEHHHHHHH-HCCCCCCEEECCCEEEEECCC
Q ss_conf             488200214454-118899788349589984166
Q gi|254780879|r  555 YVSSYNHQDAIA-KNIKAGTAVKQGQIIGWIGTT  587 (652)
Q Consensus       555 y~T~YaHlS~~a-~gV~~G~~V~qGQvIG~vGsT  587 (652)
                      +...|+-.+.+. ..++.|++|++||+||.+=+-
T Consensus       289 ~~~v~Ap~~Gi~~~~~~~G~~V~~G~~la~I~dP  322 (359)
T cd06250         289 VEMLYAPAGGMVVYRAAPGDWVEAGDVLAEILDP  322 (359)
T ss_pred             CEEEECCCCEEEEECCCCCCEECCCCEEEEEECC
T ss_conf             6799569986898727999997799989999489


No 64 
>cd06255 M14_ASTE_ASPA_like_5 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=72.30  E-value=2.9  Score=20.64  Aligned_cols=20  Identities=25%  Similarity=0.473  Sum_probs=17.6

Q ss_pred             CCCCCCEEECCCEEEEECCC
Q ss_conf             18899788349589984166
Q gi|254780879|r  568 NIKAGTAVKQGQIIGWIGTT  587 (652)
Q Consensus       568 gV~~G~~V~qGQvIG~vGsT  587 (652)
                      .++.|++|++||+||++-+-
T Consensus       245 ~v~~G~~V~kGq~lg~I~dp  264 (293)
T cd06255         245 SVPAGDTIPAGQPLGRVVDL  264 (293)
T ss_pred             ECCCCCEECCCCEEEEEECC
T ss_conf             37889997799999999899


No 65 
>LOAD_cold consensus
Probab=71.58  E-value=6.2  Score=18.38  Aligned_cols=48  Identities=27%  Similarity=0.369  Sum_probs=30.3

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCC-EEECCCEEEEE
Q ss_conf             9679996530897007999839974882002144541188997-88349589984
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGT-AVKQGQIIGWI  584 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~-~V~qGQvIG~v  584 (652)
                      .|+|..=.-..|||-.   .-.+|-.-.|-|.|.+..   .|. .++.||.|-|-
T Consensus         3 ~G~VK~f~~~kGfGFI---~~~~g~~DvFvH~s~l~~---~~~~~l~~G~~V~f~   51 (67)
T LOAD_cold         3 KGTVKWFNVKKGFGFI---TPEDGGEDVFVHQSAIQG---DGFRSLTEGQEVEFD   51 (67)
T ss_pred             CEEEEEEECCCCCEEE---EECCCCCEEEEEHHHHCC---CCCCCCCCCCEEEEE
T ss_conf             8699999899994788---757998218999478140---478647999999999


No 66 
>cd06252 M14_ASTE_ASPA_like_2 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=71.20  E-value=6.9  Score=18.06  Aligned_cols=21  Identities=29%  Similarity=0.408  Sum_probs=17.8

Q ss_pred             CCCCCCEEECCCEEEEECCCC
Q ss_conf             188997883495899841667
Q gi|254780879|r  568 NIKAGTAVKQGQIIGWIGTTG  588 (652)
Q Consensus       568 gV~~G~~V~qGQvIG~vGsTG  588 (652)
                      .++.|++|++||+||++=+..
T Consensus       258 ~v~lG~~V~kGq~lg~I~dp~  278 (316)
T cd06252         258 LVDLGDEVSAGQVAGRIHFPE  278 (316)
T ss_pred             ECCCCCEECCCCEEEEEECCC
T ss_conf             178899977999999996887


No 67 
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=70.75  E-value=6.1  Score=18.42  Aligned_cols=53  Identities=13%  Similarity=0.089  Sum_probs=38.0

Q ss_pred             CEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCC
Q ss_conf             013688417970899999749998999999998540156101699888999972788
Q gi|254780879|r  275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKD  331 (652)
Q Consensus       275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~  331 (652)
                      ......|++|||+.+|+++.|++.+.+..+    +....-..|..|-.|.++..++.
T Consensus        48 ~~~~y~~~~~d~~~Sia~~~~vt~~~~~~m----~~~~~~~~l~~~~~l~~P~~~~~  100 (423)
T COG3858          48 SGHFYDVGPGDTLTSIARTVGVTQDSAAIM----NFVICPGYLQYGLNLYIPSARKT  100 (423)
T ss_pred             CCEEEEECCCCCHHHHHHHHCCCHHHHHHH----CCCCCCCCEEEEEEEECCCCCCC
T ss_conf             534998247740433342114778898763----11146610542257852577777


No 68 
>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit; InterPro: IPR010208   The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase (IPR003667 from INTERPRO), but is distinct. This entry describes the C subunit.; GO: 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport, 0016020 membrane.
Probab=70.34  E-value=2.1  Score=21.71  Aligned_cols=17  Identities=24%  Similarity=0.135  Sum_probs=8.0

Q ss_pred             CCCCHHHHHHHHCCCCC
Q ss_conf             55650334432023332
Q gi|254780879|r  202 HTAQDEEIKNAIMNQFF  218 (652)
Q Consensus       202 ~~~~~~~~~~~~~~~~~  218 (652)
                      ..++.+++...++.++-
T Consensus       120 ~~l~~~~i~~~I~~AGI  136 (444)
T TIGR01945       120 SSLSPEEILEKIRAAGI  136 (444)
T ss_pred             HHCCHHHHHHHHHHCCC
T ss_conf             31487999999997086


No 69 
>cd06251 M14_ASTE_ASPA_like_1 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=70.26  E-value=2.8  Score=20.81  Aligned_cols=18  Identities=39%  Similarity=0.634  Sum_probs=16.0

Q ss_pred             CCCCCEEECCCEEEEECC
Q ss_conf             889978834958998416
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGs  586 (652)
                      ++.|++|++||+||++=+
T Consensus       234 ~~~G~~V~~Gq~lg~I~d  251 (287)
T cd06251         234 VKLGDKVKKGQLLATITD  251 (287)
T ss_pred             CCCCCEECCCCEEEEEEC
T ss_conf             898899479998999978


No 70 
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea.  CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA.  CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and  the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=70.11  E-value=6.1  Score=18.41  Aligned_cols=49  Identities=18%  Similarity=0.279  Sum_probs=29.7

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE
Q ss_conf             967999653089700799983997488200214454118899788349589984
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI  584 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v  584 (652)
                      .|+|..-....|||-..   -.++=.-.|-|.|.|...  --.+.+.||.+-|.
T Consensus         2 ~G~Vk~f~~~kGfGFI~---~~~~~~diF~H~s~~~~~--~~~~l~~G~~V~f~   50 (65)
T cd04458           2 TGTVKWFDDEKGFGFIT---PDDGGEDVFVHISALEGD--GFRSLEEGDRVEFE   50 (65)
T ss_pred             EEEEEEEECCCCEEEEE---ECCCCCCEEEEHHHHCCC--CCCCCCCCCEEEEE
T ss_conf             38999997999969999---579982299995892434--69747989899999


No 71 
>cd06253 M14_ASTE_ASPA_like_3 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=69.61  E-value=3.7  Score=19.99  Aligned_cols=20  Identities=35%  Similarity=0.478  Sum_probs=16.9

Q ss_pred             CCCCCCEEECCCEEEEECCC
Q ss_conf             18899788349589984166
Q gi|254780879|r  568 NIKAGTAVKQGQIIGWIGTT  587 (652)
Q Consensus       568 gV~~G~~V~qGQvIG~vGsT  587 (652)
                      -++.|++|++||+||++=+.
T Consensus       243 ~~~lG~~V~~G~~lg~I~dp  262 (298)
T cd06253         243 AKHLGDIVKRGDVIGEIVDP  262 (298)
T ss_pred             ECCCCCEECCCCEEEEEECC
T ss_conf             46889988789999999688


No 72 
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=69.17  E-value=7.6  Score=17.77  Aligned_cols=14  Identities=7%  Similarity=0.204  Sum_probs=9.4

Q ss_pred             HHCCCCCEEEEEEE
Q ss_conf             10144540688753
Q gi|254780879|r  419 EHLKPTDFLETFFS  432 (652)
Q Consensus       419 r~ir~GD~f~Vlye  432 (652)
                      .++++|+..+|.+.
T Consensus       259 ~~v~~Gq~v~I~~D  272 (348)
T PRK10476        259 KNIRVGDCATVYSM  272 (348)
T ss_pred             CCCCCCCEEEEEEE
T ss_conf             52799898999997


No 73 
>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional
Probab=69.07  E-value=3  Score=20.58  Aligned_cols=16  Identities=13%  Similarity=0.333  Sum_probs=6.6

Q ss_pred             CCCHHHHHHHHCCCCC
Q ss_conf             5650334432023332
Q gi|254780879|r  203 TAQDEEIKNAIMNQFF  218 (652)
Q Consensus       203 ~~~~~~~~~~~~~~~~  218 (652)
                      .++.+++...+.+++.
T Consensus       113 ~ls~e~i~~~L~~sGl  128 (448)
T PRK05352        113 SLSREQVKENLLESGL  128 (448)
T ss_pred             HCCHHHHHHHHHHCCC
T ss_conf             5699999999986698


No 74 
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=68.88  E-value=7.7  Score=17.73  Aligned_cols=53  Identities=15%  Similarity=0.201  Sum_probs=38.5

Q ss_pred             EEEEEECCCCCHHHHHHHC----CCCHHHHHHHHHHHHC----CCCHHHCCCCCEEEEEEC
Q ss_conf             1368841797089999974----9998999999998540----156101699888999972
Q gi|254780879|r  276 DDLIPIQHNTTIFDAMVHA----GYSNGDSAKIAKALKN----EVRVDQLTKDEILRIGVV  328 (652)
Q Consensus       276 e~~v~VK~GDTL~~IL~r~----Gvs~~ei~~i~~al~~----~~~~~~Lr~Gq~L~I~~~  328 (652)
                      -..+++++||||++|..+.    +++..+....+-.+|.    ..++++|+.|..|+|+..
T Consensus       188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~  248 (755)
T COG3170         188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA  248 (755)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCHHHHCCCCHHHCCCCCEEECCCH
T ss_conf             7666668760499998741676643199999999860915422651421334544524602


No 75 
>PRK05820 deoA thymidine phosphorylase; Reviewed
Probab=68.24  E-value=7.9  Score=17.64  Aligned_cols=57  Identities=21%  Similarity=0.295  Sum_probs=42.4

Q ss_pred             CCCCCCEEECCCCEEEEEE--------EECCCCCEE---EEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC
Q ss_conf             6796727971596799965--------308970079---998399748820021445411889978834958998416
Q gi|254780879|r  520 APRGTPIVAVGDGIVEKAN--------WAGGYGKQT---LIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       520 Ap~GTPI~Aag~G~V~~ag--------~~~GyGn~V---~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs  586 (652)
                      ++.=.+|.|..+|.|....        +.=|-|+..   .|+|.-|++-          -++.|++|++||.|..+=+
T Consensus       337 a~~~~~i~A~~~G~v~~id~~~iG~a~v~LGaGR~~~~d~ID~~vGi~l----------~~k~Gd~V~kGdpl~~iya  404 (440)
T PRK05820        337 APVIKPVYADRSGFLSAMDTRALGMAVVRLGGGRRRPGDPIDYSVGLTL----------HARLGDRVDAGEPLATLHA  404 (440)
T ss_pred             CCEEEEEECCCCEEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCCEEE----------ECCCCCEECCCCEEEEEEC
T ss_conf             8868999728966999853799999999808873678987682668588----------5158899679994999974


No 76 
>PRK10943 cold shock-like protein CspC; Provisional
Probab=67.49  E-value=6.9  Score=18.03  Aligned_cols=48  Identities=27%  Similarity=0.370  Sum_probs=31.5

Q ss_pred             CCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCC-CEEECCCEEEE
Q ss_conf             5967999653089700799983997488200214454118899-78834958998
Q gi|254780879|r  530 GDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAG-TAVKQGQIIGW  583 (652)
Q Consensus       530 g~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G-~~V~qGQvIG~  583 (652)
                      -.|+|.+-....|||-..   -.+|=.-.|-|.|.+.   ..| .....||.|-|
T Consensus         4 ~~G~VKwFn~~kGfGFI~---~~dg~~DvFvH~s~i~---~~g~~~L~eGq~V~f   52 (69)
T PRK10943          4 IKGQVKWFNESKGFGFIT---PADGSKDVFVHFSAIQ---GNGFKTLAEGQNVEF   52 (69)
T ss_pred             EEEEEEEEECCCCEEEEE---ECCCCCCEEEEHHHHC---CCCCCCCCCCCEEEE
T ss_conf             788999983999869986---1799830999938827---168832399999999


No 77 
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=66.91  E-value=7.4  Score=17.83  Aligned_cols=22  Identities=27%  Similarity=0.435  Sum_probs=14.8

Q ss_pred             CCEEEEECCCCCCCCCEEEEEE
Q ss_conf             9589984166788874268899
Q gi|254780879|r  578 GQIIGWIGTTGLSTGPHLHYEL  599 (652)
Q Consensus       578 GQvIG~vGsTG~STGPHLHfEv  599 (652)
                      -++|-.||.-++|---+|.+|+
T Consensus       471 ~eiv~lvG~d~l~~~~~l~l~~  492 (585)
T PRK04192        471 QEIVRLVGEDALSEEDRLILEV  492 (585)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHH
T ss_conf             9999864775589889789999


No 78 
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=66.40  E-value=4.6  Score=19.31  Aligned_cols=31  Identities=23%  Similarity=0.508  Sum_probs=14.6

Q ss_pred             CCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEE
Q ss_conf             89700799983997488200214454118899788
Q gi|254780879|r  541 GGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAV  575 (652)
Q Consensus       541 ~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V  575 (652)
                      |..||+|+-=|.++|-..+.+|.+    +++|+.|
T Consensus        42 G~~Gn~viaGHr~~~~~~F~~L~~----l~~GD~I   72 (137)
T cd05830          42 GEVGNFAVAGHRTTYGAPFNDLDK----LRPGDKI   72 (137)
T ss_pred             CCCCEEEEEECCCCCCCCCCCHHC----CCCCCEE
T ss_conf             999719999722897755601353----8999999


No 79 
>pfam09070 PFU PFU (PLAA family ubiquitin binding). This domain is found N terminal to pfam08324 and binds to ubiquitin.
Probab=66.28  E-value=8.6  Score=17.38  Aligned_cols=44  Identities=30%  Similarity=0.526  Sum_probs=32.8

Q ss_pred             CCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEE
Q ss_conf             700799983997488200214454118899788349589984166788874268
Q gi|254780879|r  543 YGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLH  596 (652)
Q Consensus       543 yGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLH  596 (652)
                      -|-..+||+++|-..+|.--        .|+|++-|+|++-  ++|.+.|-.+|
T Consensus         7 eGq~~~vr~~~g~veAyqWs--------~~~W~kIG~Vv~~--~~~~~~~k~~~   50 (115)
T pfam09070         7 EGQVKMVKNGDGKVEAYQWS--------EGRWVKIGDVVDG--SSGSSGGKVLY   50 (115)
T ss_pred             CCCEEEEECCCCCEEEEEEC--------CCCEEEEEEEECC--CCCCCCCCCCC
T ss_conf             77189999899969999834--------4735898889827--88877884012


No 80 
>PRK06078 pyrimidine-nucleoside phosphorylase; Reviewed
Probab=66.02  E-value=7.6  Score=17.76  Aligned_cols=57  Identities=26%  Similarity=0.263  Sum_probs=42.9

Q ss_pred             CCCCCCEEECCCCEEEEE-----E---EECCCCCEE---EEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC
Q ss_conf             679672797159679996-----5---308970079---998399748820021445411889978834958998416
Q gi|254780879|r  520 APRGTPIVAVGDGIVEKA-----N---WAGGYGKQT---LIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       520 Ap~GTPI~Aag~G~V~~a-----g---~~~GyGn~V---~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs  586 (652)
                      ++.-.+|.|.-+|.|...     |   +.=|.|+..   .|+|+-|+.-          -++.|++|++||.|..+=+
T Consensus       332 a~~~~~i~A~~~G~V~~id~~~iG~a~~~LGaGR~~~~D~ID~~vGi~l----------~~k~Gd~V~kGdpL~tiya  399 (434)
T PRK06078        332 AKYQIEVPAKESGYISEIVADEIGLAAMLLGAGRATKEDEIDLAVGIVL----------RKKVGDSVKKGESLVTIYA  399 (434)
T ss_pred             CCEEEEEECCCCEEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCCEEE----------ECCCCCEECCCCEEEEEEC
T ss_conf             8868999738865999954899999999839997888888885768487----------2569599579994999974


No 81 
>COG3608 Predicted deacylase [General function prediction only]
Probab=64.54  E-value=9.2  Score=17.15  Aligned_cols=35  Identities=26%  Similarity=0.406  Sum_probs=24.4

Q ss_pred             CCCCCEEECCCEEEEECCCCCCCCCEEEEEEE--ECCEEC
Q ss_conf             88997883495899841667888742688997--867883
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGTTGLSTGPHLHYELI--VNGIKV  606 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~--vnG~~V  606 (652)
                      |+.|++|.+||+++++=+-|+.-   +-=||+  ++|..+
T Consensus       271 v~lGd~VeaG~~la~i~~~~~~~---~~~eirA~~~G~i~  307 (331)
T COG3608         271 VDLGDKVEAGDVLATIHDPPLGE---GEAEIRAPVSGIII  307 (331)
T ss_pred             ECCCCCCCCCCEEEEEECCCCCC---CCEEEECCCCCEEE
T ss_conf             16788021787679973688887---52589727882699


No 82 
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=64.46  E-value=6  Score=18.47  Aligned_cols=14  Identities=14%  Similarity=0.420  Sum_probs=6.5

Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999998414776
Q gi|254780879|r  631 KKRINSLLNNGENP  644 (652)
Q Consensus       631 ~~~id~ll~~~~~~  644 (652)
                      .+.++.||.....|
T Consensus       605 d~~f~~LMGd~ve~  618 (635)
T COG0187         605 DEIFSTLMGDKVEP  618 (635)
T ss_pred             HHHHHHHCCCCCHH
T ss_conf             99999870778568


No 83 
>CHL00037 petA cytochrome f
Probab=64.30  E-value=9.3  Score=17.12  Aligned_cols=81  Identities=20%  Similarity=0.131  Sum_probs=48.3

Q ss_pred             CCCEEECCCCEEEEEEEECCCCCEEEE-ECCCCEEE---EEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEE
Q ss_conf             672797159679996530897007999-83997488---20021445411889978834958998416678887426889
Q gi|254780879|r  523 GTPIVAVGDGIVEKANWAGGYGKQTLI-HHGNGYVS---SYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYE  598 (652)
Q Consensus       523 GTPI~Aag~G~V~~ag~~~GyGn~V~I-~H~~Gy~T---~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfE  598 (652)
                      -|..-|...|+|.......--|..|.| +..+|-.+   .=.-..-   -|++|+.|+.||-+-.==+-|---  +..-|
T Consensus       203 N~~~~as~~G~i~~I~~~ekgg~~itI~~~~dG~~v~~~iP~Gpel---~V~eG~~vk~dqpLT~nPNVGGFG--Q~e~E  277 (320)
T CHL00037        203 NTVYNATAAGIVSKIIRKEKGGYEITIVDASDGRQVVDIIPPGPEL---LVSEGESIKLDQPLTSNPNVGGFG--QGDAE  277 (320)
T ss_pred             CCEECCCCCCEEEEEEECCCCCEEEEEEECCCCCEEEEECCCCCEE---EECCCCEEECCCCCCCCCCCCCCC--CCCEE
T ss_conf             8266055772788877657895699998658997888744999758---972798885698555699867667--66148


Q ss_pred             EEECCEECCCCEEC
Q ss_conf             97867883662000
Q gi|254780879|r  599 LIVNGIKVDSTKVR  612 (652)
Q Consensus       599 v~vnG~~VdP~~~~  612 (652)
                      |.    -.||.|++
T Consensus       278 IV----LQ~P~Rv~  287 (320)
T CHL00037        278 IV----LQDPLRVQ  287 (320)
T ss_pred             EE----ECCHHHHH
T ss_conf             99----41835846


No 84 
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=64.18  E-value=8.8  Score=17.29  Aligned_cols=48  Identities=27%  Similarity=0.354  Sum_probs=31.7

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCC-CEEECCCEEEEE
Q ss_conf             967999653089700799983997488200214454118899-788349589984
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAG-TAVKQGQIIGWI  584 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G-~~V~qGQvIG~v  584 (652)
                      .|+|..-.-.+|||-..   -.+|=.-.|.|.|.|.   ..| ...+.||.|-|.
T Consensus         3 ~G~VKwFn~~KGyGFI~---~d~gg~DvFvH~s~i~---~~G~~~L~~G~~V~f~   51 (74)
T PRK09937          3 KGTVKWFNNAKGFGFIC---PEGGGEDIFAHYSTIQ---MDGYRTLKAGQSVQFD   51 (74)
T ss_pred             CCEEEEEECCCCEEEEE---ECCCCCCEEEEHHHHC---CCCCCCCCCCCEEEEE
T ss_conf             83797883899718862---0799955999858823---1588424999999999


No 85 
>COG1278 CspC Cold shock proteins [Transcription]
Probab=64.13  E-value=6.4  Score=18.27  Aligned_cols=43  Identities=28%  Similarity=0.444  Sum_probs=31.0

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH----HCCCCCCEEE
Q ss_conf             967999653089700799983997488200214454----1188997883
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA----KNIKAGTAVK  576 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a----~gV~~G~~V~  576 (652)
                      .|+|..-...+|||-   |.-.+|=.-.|.|.|.|-    +.+.+||+|.
T Consensus         3 ~GtVKwfn~~KGfGF---I~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~   49 (67)
T COG1278           3 TGTVKWFNATKGFGF---ITPEDGGKDVFVHISAIQRAGFRTLREGQKVE   49 (67)
T ss_pred             CCEEEEEECCCCCEE---ECCCCCCCCEEEEEEEECCCCCCCCCCCCEEE
T ss_conf             616888508986337---07899985779980125127886557998899


No 86 
>pfam00529 HlyD HlyD family secretion protein.
Probab=64.09  E-value=5.1  Score=18.97  Aligned_cols=26  Identities=19%  Similarity=0.244  Sum_probs=13.8

Q ss_pred             CCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEE
Q ss_conf             007999839974882002144541188997883
Q gi|254780879|r  544 GKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVK  576 (652)
Q Consensus       544 Gn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~  576 (652)
                      +.-|+|.=.+    .|.   .+..|+.+|++|-
T Consensus       278 ~~pV~i~~~~----~~~---~~~~gl~~G~~vv  303 (304)
T pfam00529       278 GVPVEIGLDP----AFN---QSTTPLVPGEVVI  303 (304)
T ss_pred             EEEEEEEEEC----CCC---HHCCCCCCCCEEE
T ss_conf             6899999827----833---3126989998897


No 87 
>TIGR01349 PDHac_trf_mito pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006257   This group of sequences represent one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria, but not the Gram-positive bacteria.; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006090 pyruvate metabolic process, 0045254 pyruvate dehydrogenase complex.
Probab=64.05  E-value=6.3  Score=18.30  Aligned_cols=13  Identities=31%  Similarity=0.378  Sum_probs=6.7

Q ss_pred             CCCEEECCCCCCC
Q ss_conf             4200302679672
Q gi|254780879|r  513 HTGVDWAAPRGTP  525 (652)
Q Consensus       513 H~GVD~aAp~GTP  525 (652)
                      |+=||++...=||
T Consensus       441 y~~vDiSVAVatP  453 (584)
T TIGR01349       441 YKNVDISVAVATP  453 (584)
T ss_pred             ECEEEEEEEEECC
T ss_conf             1201488776568


No 88 
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=63.85  E-value=9.5  Score=17.07  Aligned_cols=33  Identities=30%  Similarity=0.345  Sum_probs=24.9

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH
Q ss_conf             967999653089700799983997488200214454
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA  566 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a  566 (652)
                      .|+|.+-.-..|||-..   -.+|=.-.|-|.|.+.
T Consensus         5 ~G~VKwF~~~kGyGFI~---~~dG~~DvFvH~s~i~   37 (69)
T PRK09507          5 KGNVKWFNESKGFGFIT---PEDGSKDVFVHFSAIQ   37 (69)
T ss_pred             EEEEEEEECCCCEEEEE---CCCCCCCEEEEHHHCC
T ss_conf             88999983999879997---0799832999907705


No 89 
>PRK09578 periplasmic multidrug efflux lipoprotein precursor; Reviewed
Probab=63.64  E-value=5.4  Score=18.77  Aligned_cols=14  Identities=7%  Similarity=0.147  Sum_probs=6.9

Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             99999999876268
Q gi|254780879|r   54 GVIIGGSLLTALDG   67 (652)
Q Consensus        54 ~~l~g~a~~~aldg   67 (652)
                      ++||+..+.++...
T Consensus        12 ~~l~~~~~L~gC~~   25 (385)
T PRK09578         12 AALVAAFALAGCGK   25 (385)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99999999816799


No 90 
>PRK09859 multidrug efflux system protein MdtE; Provisional
Probab=63.25  E-value=5.9  Score=18.50  Aligned_cols=13  Identities=38%  Similarity=0.675  Sum_probs=5.8

Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             9999999876268
Q gi|254780879|r   55 VIIGGSLLTALDG   67 (652)
Q Consensus        55 ~l~g~a~~~aldg   67 (652)
                      +|+.++++++..+
T Consensus        11 ll~~~~lL~gC~~   23 (385)
T PRK09859         11 LLFCGAMLTACDD   23 (385)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999999953799


No 91 
>pfam05651 Diacid_rec Putative sugar diacid recognition. This region is found in several proteins characterized as carbohydrate diacid regulators. An HTH DNA-binding motif is found at the C-terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=62.94  E-value=5.7  Score=18.65  Aligned_cols=60  Identities=25%  Similarity=0.342  Sum_probs=36.1

Q ss_pred             CCCCEEEEEEEECCCC-----CEEEEECCCCEEEEEHHHHHHHHCCCCCC---EEECCCEEEEECCCCC
Q ss_conf             1596799965308970-----07999839974882002144541188997---8834958998416678
Q gi|254780879|r  529 VGDGIVEKANWAGGYG-----KQTLIHHGNGYVSSYNHQDAIAKNIKAGT---AVKQGQIIGWIGTTGL  589 (652)
Q Consensus       529 ag~G~V~~ag~~~GyG-----n~V~I~H~~Gy~T~YaHlS~~a~gV~~G~---~V~qGQvIG~vGsTG~  589 (652)
                      -.+|+++.+|...=-|     =.-.|+++.. ...|.....-.+|+|+|-   -+-+|++||-+|-||-
T Consensus        25 d~~G~IIAS~d~~RiG~~HegA~~vi~~~~~-~~i~~~~~~~~~G~k~GiNlPi~~~g~viGvIGITG~   92 (135)
T pfam05651        25 DEQGVIIASGDPSRIGQFHEGALLALREGRV-VEIDAADASRLKGVKPGINLPIIFQGEVIGVIGITGE   92 (135)
T ss_pred             CCCCEEEECCCHHHCCCHHHHHHHHHHCCCE-EEECHHHHHHCCCCCCCCEECEEECCEEEEEEEEECC
T ss_conf             9997799608856572232999999973991-8985767744579887512586989999999996289


No 92 
>cd06850 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
Probab=62.12  E-value=5.9  Score=18.55  Aligned_cols=20  Identities=25%  Similarity=0.421  Sum_probs=15.3

Q ss_pred             CCCCCEEECCCEEEEECCCC
Q ss_conf             88997883495899841667
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGTTG  588 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGsTG  588 (652)
                      |+.|++|+.||+++.+-+--
T Consensus        15 V~~Gd~V~~G~~l~~iE~mK   34 (67)
T cd06850          15 VKEGDKVEAGQPLAVLEAMK   34 (67)
T ss_pred             ECCCCEECCCCEEEEEEECC
T ss_conf             57999997899999999366


No 93 
>PRK05035 electron transport complex protein RnfC; Provisional
Probab=62.05  E-value=4.9  Score=19.10  Aligned_cols=14  Identities=21%  Similarity=0.109  Sum_probs=5.9

Q ss_pred             CCHHHHHHHHCCCC
Q ss_conf             65033443202333
Q gi|254780879|r  204 AQDEEIKNAIMNQF  217 (652)
Q Consensus       204 ~~~~~~~~~~~~~~  217 (652)
                      ++.++....+++.+
T Consensus       131 ~~~~el~~~I~~AG  144 (725)
T PRK05035        131 LSREELIERIRQAG  144 (725)
T ss_pred             CCHHHHHHHHHHCC
T ss_conf             89999999999759


No 94 
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=60.43  E-value=5.8  Score=18.59  Aligned_cols=56  Identities=20%  Similarity=0.278  Sum_probs=33.6

Q ss_pred             CCCCCEEEEECCCCE-EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCEEC
Q ss_conf             897007999839974-882002144541188997883495899841667888742688997867883662000
Q gi|254780879|r  541 GGYGKQTLIHHGNGY-VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKVR  612 (652)
Q Consensus       541 ~GyGn~V~I~H~~Gy-~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~~  612 (652)
                      .|-||+|+--|..++ -+.+.+|..    +++|+.|       ++-+.+    --..|+|... .-|+|-.+.
T Consensus        39 ~G~gN~viaGH~~~~~~~~F~~L~~----l~~GD~I-------~v~~~~----~~~~Y~V~~~-~iV~p~d~~   95 (127)
T cd06165          39 MGKGNYALAGHNMRNKGVLFSPLYK----VKVGDKI-------YLTDKD----NVYEYKVTSK-KIVDPTRVD   95 (127)
T ss_pred             CCCCCEEEEECCCCCCCCCCCCHHH----CCCCCEE-------EEEECC----CEEEEEEEEE-EEECCCCCE
T ss_conf             9988699993658867654667656----8999999-------999899----3999999489-999988777


No 95 
>PRK11556 multidrug efflux system subunit MdtA; Provisional
Probab=59.89  E-value=7.1  Score=17.94  Aligned_cols=19  Identities=11%  Similarity=0.263  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899989899999999999999987
Q gi|254780879|r   40 LRWLSTTFFAGITSGVIIGGSLLT   63 (652)
Q Consensus        40 ~rw~~~t~ltg~~~~~l~g~a~~~   63 (652)
                      +|||.-.++     .+++|++.|-
T Consensus         7 ~~~~~~~~~-----~~~~~~~~~~   25 (415)
T PRK11556          7 FRWVIVIVV-----VIAAIAAFWF   25 (415)
T ss_pred             HHHHHHHHH-----HHHHHHHHHH
T ss_conf             589999999-----9999999987


No 96 
>PRK10559 p-hydroxybenzoic acid efflux subunit AaeA; Provisional
Probab=56.29  E-value=13  Score=16.19  Aligned_cols=14  Identities=7%  Similarity=0.105  Sum_probs=7.8

Q ss_pred             CHHHCCCCCEEEEE
Q ss_conf             61016998889999
Q gi|254780879|r  313 RVDQLTKDEILRIG  326 (652)
Q Consensus       313 ~~~~Lr~Gq~L~I~  326 (652)
                      .+..+++||...|.
T Consensus       201 qL~~ir~Gq~v~I~  214 (310)
T PRK10559        201 KLEGVRPGYRAEIT  214 (310)
T ss_pred             HCCCCCCCCEEEEE
T ss_conf             12538999979999


No 97 
>COG1155 NtpA Archaeal/vacuolar-type H+-ATPase subunit A [Energy production and conversion]
Probab=55.78  E-value=9.3  Score=17.15  Aligned_cols=26  Identities=23%  Similarity=0.176  Sum_probs=18.8

Q ss_pred             ECCCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             41797089999974999899999999
Q gi|254780879|r  281 IQHNTTIFDAMVHAGYSNGDSAKIAK  306 (652)
Q Consensus       281 VK~GDTL~~IL~r~Gvs~~ei~~i~~  306 (652)
                      |--|.|+..-.++.|++..-.+.-..
T Consensus       306 IYtGiTiaEY~RDmGy~v~lmADSTS  331 (588)
T COG1155         306 IYTGITIAEYYRDMGYDVALMADSTS  331 (588)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCHHH
T ss_conf             53223199988763025677501389


No 98 
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=55.70  E-value=5.9  Score=18.51  Aligned_cols=137  Identities=14%  Similarity=0.098  Sum_probs=78.6

Q ss_pred             EEEEECCCC-CHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE-CCCCCCCEEEEE--EECCCCCEEEEEE
Q ss_conf             368841797-089999974999899999999854015610169988899997-278886405899--9716883489998
Q gi|254780879|r  277 DLIPIQHNT-TIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV-VQKDDKFTIVRF--SIYHKQKHLLTIA  352 (652)
Q Consensus       277 ~~v~VK~GD-TL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~-~~~~~~~~~~r~--si~~~~~~~~~va  352 (652)
                      -.++..+|+ ++..|=-||.=+..++-.       ..++ .|++|+.|=|.. +.+| +.++.++  .+|.-..-.+.+.
T Consensus       455 aalP~l~G~i~F~nirFRY~pD~PeVL~-------nl~L-~I~~Ge~IGIvGpSGSG-KSTLTKL~QRLYtP~~GqVLVD  525 (703)
T TIGR01846       455 AALPELKGSITFENIRFRYKPDSPEVLS-------NLSL-DIKPGEVIGIVGPSGSG-KSTLTKLLQRLYTPEHGQVLVD  525 (703)
T ss_pred             CCCCCCCCCEEEEEEEECCCCCCCHHHH-------CCCC-CCCCCEEEEEECCCCCC-HHHHHHHHHHHCCCCCCEEEEC
T ss_conf             0354225726787533146888717873-------2687-65786579987278986-7899999886148888747770


Q ss_pred             ECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEE
Q ss_conf             42788432013332100000122111233454211025666887199989999999973011101210144540688
Q gi|254780879|r  353 LNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTDFLET  429 (652)
Q Consensus       353 ~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD~f~V  429 (652)
                      --|-.    -.+|....++.-..--........|.|+|.  ..+-++|..-+--.++ ++---||...++.|=.-+|
T Consensus       526 G~DLA----~~DP~wLRRQ~gVVLQEn~LFsrSirdNI~--l~~P~~~~E~Vi~AA~-LAGA~dFI~~Lp~GY~T~v  595 (703)
T TIGR01846       526 GVDLA----IADPAWLRRQVGVVLQENVLFSRSIRDNIA--LCNPGASVEHVIAAAK-LAGAHDFISELPQGYNTEV  595 (703)
T ss_pred             CCCCC----CCCCCHHHHCCEEEEECCHHHCCCHHHHHH--HCCCCCCHHHHHHHHH-HCCHHHHHHHCCCCCCCCC
T ss_conf             30001----018520102230234000210122788985--1777769899999986-2185899973637677400


No 99 
>PRK10218 GTP-binding protein; Provisional
Probab=54.93  E-value=12  Score=16.27  Aligned_cols=43  Identities=26%  Similarity=0.417  Sum_probs=34.8

Q ss_pred             CEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEEEEECCC
Q ss_conf             079998399748820021445411---8899788349589984166
Q gi|254780879|r  545 KQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQIIGWIGTT  587 (652)
Q Consensus       545 n~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvIG~vGsT  587 (652)
                      |=+.|-+.+|-.|.|+-.+--.+|   |.+|..|=.|+|||.---.
T Consensus       485 ~G~lis~~~g~~t~yal~~lq~rg~lfv~pg~~vy~GmivGe~~r~  530 (607)
T PRK10218        485 NGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRS  530 (607)
T ss_pred             CEEEEECCCCEEHHHHHHHHHHCCCEEECCCCCEECCEEEEEECCC
T ss_conf             5137975776178987753875453673699966887586760786


No 100
>cd06663 Biotinyl_lipoyl_domains Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue.
Probab=53.93  E-value=9.9  Score=16.93  Aligned_cols=17  Identities=35%  Similarity=0.556  Sum_probs=7.7

Q ss_pred             CCCCCEEECCCEEEEEC
Q ss_conf             88997883495899841
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIG  585 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vG  585 (652)
                      +++|++|++||.+..+=
T Consensus        21 v~~Gd~V~~Gd~l~~iE   37 (73)
T cd06663          21 KKVGDKVKKGDVLAEIE   37 (73)
T ss_pred             ECCCCEECCCCEEEEEE
T ss_conf             26999997999999999


No 101
>pfam00364 Biotin_lipoyl Biotin-requiring enzyme. This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the model may not recognize the Glycine cleavage system H proteins.
Probab=53.88  E-value=9.9  Score=16.93  Aligned_cols=18  Identities=33%  Similarity=0.571  Sum_probs=9.1

Q ss_pred             CCCCCEEECCCEEEEECC
Q ss_conf             889978834958998416
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGs  586 (652)
                      +++|+.|++||.|..+-+
T Consensus        21 v~~Gd~V~~g~~l~~iEt   38 (73)
T pfam00364        21 VKVGDKVKAGQVLCEVEA   38 (73)
T ss_pred             ECCCCEECCCCEEEEEEE
T ss_conf             589899928998999996


No 102
>TIGR02472 sucr_P_syn_N sucrose-phosphate synthase, putative, glycosyltransferase domain; InterPro: IPR012822    This family consists of the N-terminal regions, or in some cases the entirety, of bacterial proteins closely related to plant sucrose-phosphate synthases (SPS). The C-terminal domain (IPR012821 from INTERPRO), found with most members of this family, resembles both bona fide plant sucrose-phosphate phosphatases (SPP) and the SPP-like domain of plant sucrose phosphate synthase (SPS). At least two members of this family lack the SPP-like domain, which may have binding or regulatory rather than enzymatic activity by analogy to plant SPS. This enzyme produces sucrose 6-phosphate and UDP from UDP-glucose and D-fructose 6-phosphate, and may be encoded near the gene for fructokinase..
Probab=51.86  E-value=5.2  Score=18.94  Aligned_cols=26  Identities=46%  Similarity=0.607  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCC
Q ss_conf             102356764143404434642003026796727971596
Q gi|254780879|r  494 RMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDG  532 (652)
Q Consensus       494 risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G  532 (652)
                      -+|-|||--.             ==||.+|=||+|+.||
T Consensus       354 ALTEPFGLTL-------------lEAAAcGLPivAT~DG  379 (445)
T TIGR02472       354 ALTEPFGLTL-------------LEAAACGLPIVATEDG  379 (445)
T ss_pred             CCCCCCHHHH-------------HHHHHCCCCEEECCCC
T ss_conf             2125301689-------------9999769972107864


No 103
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=51.59  E-value=9.7  Score=16.99  Aligned_cols=81  Identities=20%  Similarity=0.209  Sum_probs=39.2

Q ss_pred             CEEECCCCCCCEEECCCCEEEEEEEE--CCCCCEEEEECCCCE-EEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCC
Q ss_conf             00302679672797159679996530--897007999839974-882002144541188997883495899841667888
Q gi|254780879|r  515 GVDWAAPRGTPIVAVGDGIVEKANWA--GGYGKQTLIHHGNGY-VSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLST  591 (652)
Q Consensus       515 GVD~aAp~GTPI~Aag~G~V~~ag~~--~GyGn~V~I~H~~Gy-~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~ST  591 (652)
                      ++++..-.||-=.+-..|...+.+..  |..||+|+--|...+ -+.+.||.+    +++|++|.      .  .++.. 
T Consensus        12 ~~~~pi~~g~~~~~L~~G~g~~~~t~~PG~~gN~viaGH~~~~~~~~F~~L~~----l~~GD~I~------l--~~~~~-   78 (126)
T cd06166          12 DLKLPILEGTDEENLKYALGHFENTAMPGENGNFAIAGHRSYTYGRIFNRLDE----VEKGDEIK------V--TTKNG-   78 (126)
T ss_pred             CCEEEEEECCCHHHHHCCCEEECCCCCCCCCCCEEEEEEECCCCCCCCCCHHH----CCCCCEEE------E--EECCE-
T ss_conf             98868994899899812657623888899996299997508887855200551----85899999------9--99998-


Q ss_pred             CCEEEEEEEECCEECCCCEE
Q ss_conf             74268899786788366200
Q gi|254780879|r  592 GPHLHYELIVNGIKVDSTKV  611 (652)
Q Consensus       592 GPHLHfEv~vnG~~VdP~~~  611 (652)
                        -.+|+|... +-|+|-.+
T Consensus        79 --~y~Y~V~~~-~iV~p~d~   95 (126)
T cd06166          79 --TYKYKITSI-FVVEPTDT   95 (126)
T ss_pred             --EEEEEEEEE-EEECCCCC
T ss_conf             --999999779-99997655


No 104
>pfam02241 MCR_beta Methyl-coenzyme M reductase beta subunit, C-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (pfam02249), 2 beta (this family), and 2 gamma (pfam2240) subunits with two identical nickel porphinoid active sites. The C-terminal domain of MCR beta has an all-alpha fold with buried central helix.
Probab=50.93  E-value=13  Score=16.18  Aligned_cols=46  Identities=20%  Similarity=0.200  Sum_probs=28.9

Q ss_pred             CCCCCEEECCCCCCCEEECCCCEEEEEEEE-C-CCCCEEEEECCCCEE
Q ss_conf             464200302679672797159679996530-8-970079998399748
Q gi|254780879|r  511 RMHTGVDWAAPRGTPIVAVGDGIVEKANWA-G-GYGKQTLIHHGNGYV  556 (652)
Q Consensus       511 r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-~-GyGn~V~I~H~~Gy~  556 (652)
                      .---|+||.-..||-|--.-=---||-|-. | -+||.|+-||..|+-
T Consensus       155 TgLPg~D~Gr~~GtaVgfSFFSHSIYGGGGPGiFnGNHvVTRHskG~a  202 (255)
T pfam02241       155 TGLPGVDFGRAEGTAVGFSFFSHSIYGGGGPGIFHGNHIVTRHSKGFA  202 (255)
T ss_pred             CCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCC
T ss_conf             289986554202225322311001005898865148757884478732


No 105
>PRK03140 phosphatidylserine decarboxylase; Provisional
Probab=50.09  E-value=16  Score=15.53  Aligned_cols=35  Identities=14%  Similarity=0.027  Sum_probs=20.3

Q ss_pred             HHHHHHHCCCCHHHHHHHHH---HHHCCCCHHHCCCCCE
Q ss_conf             89999974999899999999---8540156101699888
Q gi|254780879|r  287 IFDAMVHAGYSNGDSAKIAK---ALKNEVRVDQLTKDEI  322 (652)
Q Consensus       287 L~~IL~r~Gvs~~ei~~i~~---al~~~~~~~~Lr~Gq~  322 (652)
                      +-.-.+.++++-+|+.+=+.   +++..+ .++|++|.+
T Consensus        35 I~~fik~~~In~~E~~~~~~~Y~sfndFF-tR~Lk~g~R   72 (259)
T PRK03140         35 IPSYAKVFQINQDEMEKGLKEYRTLHELF-TRKLKEGKR   72 (259)
T ss_pred             HHHHHHHHCCCHHHHHCCHHHCCCHHHHH-HCCCCCCCC
T ss_conf             99999997979899636964489889962-104678986


No 106
>PRK03934 phosphatidylserine decarboxylase; Provisional
Probab=49.38  E-value=7.2  Score=17.93  Aligned_cols=17  Identities=59%  Similarity=0.812  Sum_probs=13.1

Q ss_pred             CCCCCCEEECCCEEEEE
Q ss_conf             18899788349589984
Q gi|254780879|r  568 NIKAGTAVKQGQIIGWI  584 (652)
Q Consensus       568 gV~~G~~V~qGQvIG~v  584 (652)
                      .+++|++|+.||.||.+
T Consensus       250 ~l~~g~~Vk~Gq~ig~~  266 (267)
T PRK03934        250 NLKAGESVKFGESIGKI  266 (267)
T ss_pred             CCCCCCEEEEEHHHCCC
T ss_conf             67899998820432014


No 107
>TIGR03257 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=49.28  E-value=13  Score=16.01  Aligned_cols=51  Identities=22%  Similarity=0.214  Sum_probs=31.0

Q ss_pred             CCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEE-C-CCCCEEEEECCCCEE
Q ss_conf             40443464200302679672797159679996530-8-970079998399748
Q gi|254780879|r  506 ILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWA-G-GYGKQTLIHHGNGYV  556 (652)
Q Consensus       506 ilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~-~-GyGn~V~I~H~~Gy~  556 (652)
                      ++-+-.---|+||.-..||-|--.-=---||-|-. | -+||+|+-||..|+-
T Consensus       334 llE~ETGLPG~D~Gr~~GtaVgfSFFSHSIYGGGGPGiFnGNHVVTRHskG~a  386 (433)
T TIGR03257       334 ILEKETGLPGVDYGRVEGTAVGFSFFSHSIYGGGGPGIFNGNHVVTRHSKGFA  386 (433)
T ss_pred             HHHHHCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCEEEEECCCCCC
T ss_conf             56661289987555412135423310002106898865058757883478732


No 108
>pfam10262 Rdx Rdx family. This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown. Selenoprotein W contains selenium as selenocysteine in the primary protein structure and levels of this selenoprotein are affected by selenium.
Probab=48.91  E-value=16  Score=15.40  Aligned_cols=54  Identities=19%  Similarity=0.112  Sum_probs=35.1

Q ss_pred             EEEEEC--CCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCC
Q ss_conf             799983--9974882002144541188997883495899841667888742688997867883662
Q gi|254780879|r  546 QTLIHH--GNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDST  609 (652)
Q Consensus       546 ~V~I~H--~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~  609 (652)
                      .|.|.+  ..||..+|..|+..... +-++.+  .++-...|++|       -|||.+||.-|=-.
T Consensus         2 ~V~I~YC~~Cg~~~ra~~l~qeLl~-~f~~~i--~~v~l~p~~~G-------~FeV~v~~~li~sk   57 (76)
T pfam10262         2 KVTIEYCTQCGWLLRAAWLAQELLS-TFPDDL--IEVELQPGTGG-------AFEVTVNGELIWSK   57 (76)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH-HCCCHH--HEEEEEECCCC-------EEEEEECCEEEEEE
T ss_conf             1899987888981899999999998-776400--15886647993-------59999999998983


No 109
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=48.79  E-value=11  Score=16.55  Aligned_cols=31  Identities=23%  Similarity=0.462  Sum_probs=17.9

Q ss_pred             CCCCCEEEEECCCCE-EEEEHHHHHHHHCCCCCCEE
Q ss_conf             897007999839974-88200214454118899788
Q gi|254780879|r  541 GGYGKQTLIHHGNGY-VSSYNHQDAIAKNIKAGTAV  575 (652)
Q Consensus       541 ~GyGn~V~I~H~~Gy-~T~YaHlS~~a~gV~~G~~V  575 (652)
                      |.-||+|+--|..++ .+.+.+|..    +++|+.|
T Consensus        40 g~~gN~vIaGH~~~~~~~~F~~L~~----l~~GD~i   71 (128)
T cd00004          40 GENGNTVIAGHRGGDSGTVFSDLDN----LKKGDKI   71 (128)
T ss_pred             CCCCCEEEEEEECCCCCCCCCCHHH----CCCCCEE
T ss_conf             9996099999818998844365545----7689989


No 110
>KOG3962 consensus
Probab=48.78  E-value=16  Score=15.39  Aligned_cols=71  Identities=21%  Similarity=0.254  Sum_probs=35.8

Q ss_pred             CCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCC
Q ss_conf             64200302679672797159679996530897007999839974882002144541188997883495899841667
Q gi|254780879|r  512 MHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTG  588 (652)
Q Consensus       512 ~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG  588 (652)
                      +|.-+|  .|--++|+++-.=-=-.+.-.+|||+|+-|.- +|.+  |+-...+. .-..+.-|-|++-.+.+-|+|
T Consensus        73 ph~~~~--gp~p~e~f~avki~dsrIaLKsGyGKYlsins-dglv--vg~qeAvG-~~EQw~~vFq~~r~a~~as~s  143 (246)
T KOG3962          73 PHDEVD--GPEPEEQFMAVKISDSRIALKSGYGKYLSINS-DGLV--VGRQEAVG-SREQWEPVFQEGRMALLASNS  143 (246)
T ss_pred             CCCCCC--CCCCCHHEEEEECCCCEEEEECCCCCEEEECC-CCCE--EEEHHHCC-CHHHCHHHHHCCCEEEEECCC
T ss_conf             775456--89971007999736864773046551566547-7637--87434318-565330134236267663266


No 111
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=48.52  E-value=10  Score=16.76  Aligned_cols=14  Identities=21%  Similarity=0.335  Sum_probs=8.2

Q ss_pred             CCCCCEEEEECCCC
Q ss_conf             89700799983997
Q gi|254780879|r  541 GGYGKQTLIHHGNG  554 (652)
Q Consensus       541 ~GyGn~V~I~H~~G  554 (652)
                      |.-||+|+--|.+.
T Consensus        41 G~~GN~viaGH~~~   54 (127)
T cd05828          41 GEGGNIVIAGHRDT   54 (127)
T ss_pred             CCCCCEEEEEECCC
T ss_conf             98886999950688


No 112
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=48.06  E-value=13  Score=16.02  Aligned_cols=16  Identities=25%  Similarity=0.638  Sum_probs=11.6

Q ss_pred             CCCCCEEECCCEEEEE
Q ss_conf             8899788349589984
Q gi|254780879|r  569 IKAGTAVKQGQIIGWI  584 (652)
Q Consensus       569 V~~G~~V~qGQvIG~v  584 (652)
                      +++|+.|..||++..+
T Consensus        55 v~~Gd~V~~Gd~L~~I   70 (71)
T PRK05889         55 VSVGDVIQAGDLIAVI   70 (71)
T ss_pred             ECCCCEECCCCEEEEE
T ss_conf             7899998899999996


No 113
>pfam10165 Ric8 Guanine nucleotide exchange factor synembryn. Ric8 is involved in the EGL-30 neurotransmitter signalling pathway. It is a guanine nucleotide exchange factor that regulates neurotransmitter secretion.
Probab=47.56  E-value=6  Score=18.49  Aligned_cols=84  Identities=10%  Similarity=0.092  Sum_probs=43.4

Q ss_pred             EEEHHHHHHHHCCCCCCEEECCCEEEEECC-CCCCCCCEEEEEEEECCEECCCCEE-CCCC--CCCCCHHHHHHHHHHHH
Q ss_conf             820021445411889978834958998416-6788874268899786788366200-0788--78788899999999999
Q gi|254780879|r  557 SSYNHQDAIAKNIKAGTAVKQGQIIGWIGT-TGLSTGPHLHYELIVNGIKVDSTKV-RIPE--RENLKGDLLQRFAMEKK  632 (652)
Q Consensus       557 T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs-TG~STGPHLHfEv~vnG~~VdP~~~-~lp~--~~~l~~~~l~~F~~~~~  632 (652)
                      |-|+|.++|.  .+.|--.-++-.-+|... ++..|.+-     ...+..|||.+= ..|.  ..++++  |.+=+||++
T Consensus       337 ~GYGnAAGlL--a~rgll~~~~~~~~ySsd~edsdteey-----~~~~~~INPVTG~~~~~e~~n~~~~--MTeEeKE~E  407 (438)
T pfam10165       337 IGYGNAAGLL--ANRGLLGPGRAQEAYSSDSEDSDTEEY-----KSAKRAINPITGQVEDAEKPNPMEG--MTEEEKERE  407 (438)
T ss_pred             CCCHHHHHHH--HHCCCCCCCCCCCCCCCCCCCCCHHHH-----HHCCCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHH
T ss_conf             4851789999--874887887654234678776530456-----6406777987687678778999887--898899999


Q ss_pred             --HHHHHHHCCC-----CCCCCEE
Q ss_conf             --9999984147-----7667534
Q gi|254780879|r  633 --RINSLLNNGE-----NPKKPLF  649 (652)
Q Consensus       633 --~id~ll~~~~-----~~~~~~~  649 (652)
                        |+-.|+++..     .|..|+.
T Consensus       408 AerL~~LfdrL~~~GvIq~~npv~  431 (438)
T pfam10165       408 AERLFVLFERLKKTGVVQVENPVA  431 (438)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf             999999999998669767886688


No 114
>PRK04599 consensus
Probab=47.46  E-value=14  Score=15.81  Aligned_cols=32  Identities=9%  Similarity=0.254  Sum_probs=20.9

Q ss_pred             CCCEEEEEHH-HHHHHHCCCCCCEEECCCEEEE
Q ss_conf             9974882002-1445411889978834958998
Q gi|254780879|r  552 GNGYVSSYNH-QDAIAKNIKAGTAVKQGQIIGW  583 (652)
Q Consensus       552 ~~Gy~T~YaH-lS~~a~gV~~G~~V~qGQvIG~  583 (652)
                      |...+..+.- .-++...+++|++|+-||.||.
T Consensus       251 GSTVIllF~~~~~~~~~~l~~g~~vrmGq~la~  283 (285)
T PRK04599        251 GSTVINLFAKDAIRFDESMANGQPTRMGTPYAH  283 (285)
T ss_pred             CCEEEEEECCCCCCCCHHCCCCCEEECCCCCCC
T ss_conf             884999926998551000688998751831015


No 115
>TIGR01394 TypA_BipA GTP-binding protein TypA; InterPro: IPR006298   This bacterial (and Arabidopsis) protein, termed TypA or BipA, is a GTP-binding protein. It is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.; GO: 0005525 GTP binding, 0005622 intracellular.
Probab=46.67  E-value=17  Score=15.29  Aligned_cols=199  Identities=18%  Similarity=0.212  Sum_probs=89.1

Q ss_pred             HHHHH-HHCCCCHHHHHHHHHHHCCCCHHHH-HCCCCCEEE----------EEEEEECCCCC--CCCCCCEEEEEEECCC
Q ss_conf             56668-8719998999999997301110121-014454068----------87532115785--1246723688962388
Q gi|254780879|r  390 IWRAT-SFNGMNSNLVKLIMRTLASSVNLQE-HLKPTDFLE----------TFFSVNHANNQ--ASDDSELLYIHARFGE  455 (652)
Q Consensus       390 Ly~aa-~~~gip~~ii~~lv~i~a~dVDFqr-~ir~GD~f~----------Vlye~~~~~g~--~~~~geil~A~~~~~g  455 (652)
                      |+..- -+.--+..+-.+|.+-+..+|-..- +...-|.|+          |+.|.+-.+|-  .++.+++.|-.  ..|
T Consensus       326 lAG~EVGk~VTSR~i~dRL~rEL~~NvALrVe~t~~~D~f~VsGRGELhLsILiEtMRREGfEl~Vg~P~Vi~k~--~dG  403 (609)
T TIGR01394       326 LAGKEVGKFVTSRQIRDRLERELETNVALRVEDTESADKFEVSGRGELHLSILIETMRREGFELQVGRPQVIYKE--IDG  403 (609)
T ss_pred             CCCCCCCCEECCCCHHHHHHHHHHCCCEEEEECCCCCCCEEEECCEEEHHHHHHHCCCCCCEEEEECCCEEEEEE--ECC
T ss_conf             655325730324415789999863171456403898873487201113023454203444414753597789984--588


Q ss_pred             CCCCCCCCCCCC--CCCCCCCCCCCCCHHHCCCC--CCCCC-CCCCCCCC-CCCCCCCCCCCCCCCEEECCCCCCCEEEC
Q ss_conf             542013455766--55444335566100000112--33345-41023567-64143404434642003026796727971
Q gi|254780879|r  456 TRTRFYRFLNPV--DGSVEYFNENGKSSRPFLLR--TPVPF-GRMTSGFG-MRYHPILGYSRMHTGVDWAAPRGTPIVAV  529 (652)
Q Consensus       456 ~~~~~yrf~~~~--~~~~~yyd~~G~S~~k~llr--~Pv~~-~risS~Fg-~R~hPilg~~r~H~GVD~aAp~GTPI~Aa  529 (652)
                      +....|-.-+-+  +...+.. -+--+.||+-|.  .|... ||++=-|- +-| ...||    .+-=...-+||=|+..
T Consensus       404 ~k~EP~E~~~IDVPEe~~G~V-~e~Lg~RKgEm~~M~~~g~EG~tRl~F~~PsR-GLIGf----r~~FlT~TrG~Gimn~  477 (609)
T TIGR01394       404 KKLEPIEELTIDVPEEHVGAV-IEKLGKRKGEMKDMEPSGNEGRTRLEFVIPSR-GLIGF----RTEFLTDTRGTGIMNH  477 (609)
T ss_pred             EEECCEEEEEEECCCCCCCHH-HHHHCCCCEEEEECCCCCCCCEEEEEEECCCC-CHHHH----HHHHHHHHHHHHHHHH
T ss_conf             531875699980285335466-65314783477725676996469999981664-00122----0245441021311201


Q ss_pred             CCCEEEEEEEE-C---CCCCEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEEEEECCCCCCCCCEEEEEEEEC
Q ss_conf             59679996530-8---970079998399748820021445411---8899788349589984166788874268899786
Q gi|254780879|r  530 GDGIVEKANWA-G---GYGKQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVN  602 (652)
Q Consensus       530 g~G~V~~ag~~-~---GyGn~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vn  602 (652)
                      -  =-.|.=|. |   .-=|=+.|--.+|-.|.||=+|-=-||   |.+|++|=+|+|||-==              |-|
T Consensus       478 ~--F~~Y~P~~pG~i~~R~~GsLVs~~~G~a~~YaL~nLqeRG~~Fv~pG~~VY~GMIiGEhs--------------R~~  541 (609)
T TIGR01394       478 V--FDEYEPWKPGEIETRRNGSLVSMEDGTATAYALWNLQERGRLFVSPGTEVYEGMIIGEHS--------------REN  541 (609)
T ss_pred             H--HHCCCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCEEECCCCCEECCEEEEECC--------------CCC
T ss_conf             2--102578887687775141589926881066768738753843307886263347887238--------------866


Q ss_pred             CEECCCCEEC
Q ss_conf             7883662000
Q gi|254780879|r  603 GIKVDSTKVR  612 (652)
Q Consensus       603 G~~VdP~~~~  612 (652)
                      -=-|||+|-|
T Consensus       542 DL~VN~~K~K  551 (609)
T TIGR01394       542 DLDVNVCKAK  551 (609)
T ss_pred             CCEECCCCCC
T ss_conf             6602751676


No 116
>pfam08596 Lgl_C Lethal giant larvae(Lgl) like, C-terminal. The Lethal giant larvae (Lgl) tumour suppressor family is conserved from yeast to mammals. The Lgl family functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface. The N-terminal half of Lgl members contains WD40 repeats (see pfam00400), while the C-terminal half appears specific to the family.
Probab=46.24  E-value=8.2  Score=17.53  Aligned_cols=142  Identities=18%  Similarity=0.228  Sum_probs=61.8

Q ss_pred             CCCCCCC-CCCCCCCC-CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHH--HHH
Q ss_conf             3345410-23567641-4340443464200302679672797159679996530897007999839974882002--144
Q gi|254780879|r  489 PVPFGRM-TSGFGMRY-HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNH--QDA  564 (652)
Q Consensus       489 Pv~~~ri-sS~Fg~R~-hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaH--lS~  564 (652)
                      ++++-.+ +|.-+-|. .|..... -|+-.|..      +...+--+|.+  -..+.|..++.=+.+|..-+|.=  |..
T Consensus       224 ~i~g~vva~s~~~iRv~kp~~sK~-~hK~~~~~------~~c~~a~vv~~--~~~~~g~~LV~l~~~g~~k~ySlP~LkE  294 (393)
T pfam08596       224 VIPGFVVATSVSDIRVFKPGKSKG-THKSFDYP------ILCSGASVVPT--GQRKHGIVLVALFINGSIKVYSLPSLKE  294 (393)
T ss_pred             EEEEEEEEECCCCEEEECCCCCCC-CCEEECCC------EECCEEEEEEE--CCCCCCEEEEEEECCCCEEEEECCCHHH
T ss_conf             541499998677607972766655-41000363------02140599762--1357706999996698189983676365


Q ss_pred             H-----H-----HCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCE----------ECCCCEECCCCCCCCCHHHH
Q ss_conf             5-----4-----11889978834958998416678887426889978678----------83662000788787888999
Q gi|254780879|r  565 I-----A-----KNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGI----------KVDSTKVRIPERENLKGDLL  624 (652)
Q Consensus       565 ~-----a-----~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~----------~VdP~~~~lp~~~~l~~~~l  624 (652)
                      |     .     +..+...--+-|++++++|.+-.+   .++  ++-.|+          -.||-. .+|..-....-+-
T Consensus       295 i~~~~lp~~~~~~~~~~s~i~~~GDi~~~~gp~E~~---l~~--v~g~~~~~~~~~~~D~l~Np~~-~iPpRPtis~lqW  368 (393)
T pfam08596       295 IKKMKLPFPIDARYLSESSILRNGDIFIRTGPTEAA---LIS--VFGSSSTGAELPPTDLLYNPNA-AIPPRPQVSSLQW  368 (393)
T ss_pred             HCCCCCCCCCCCCCCCCCEECCCCCEEEECCCCCEE---EEE--EECCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCC
T ss_conf             401468866575533474682899989861874168---999--8647654567896010348445-6899885420012


Q ss_pred             HHHHH--HHHHHHHHHHCCCCCC
Q ss_conf             99999--9999999984147766
Q gi|254780879|r  625 QRFAM--EKKRINSLLNNGENPK  645 (652)
Q Consensus       625 ~~F~~--~~~~id~ll~~~~~~~  645 (652)
                      ....+  -.+.+|.||.-..+|+
T Consensus       369 ~~GtqyvS~~dld~LigGp~RPp  391 (393)
T pfam08596       369 ARGTQYCSPEDLDLLIGGPNRPP  391 (393)
T ss_pred             CCCCEEECHHHHHHHHCCCCCCC
T ss_conf             13506509999999857999998


No 117
>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=46.13  E-value=15  Score=15.71  Aligned_cols=15  Identities=13%  Similarity=0.242  Sum_probs=8.5

Q ss_pred             CEEECCCCEEEEEEE
Q ss_conf             279715967999653
Q gi|254780879|r  525 PIVAVGDGIVEKANW  539 (652)
Q Consensus       525 PI~Aag~G~V~~ag~  539 (652)
                      -|+--.+|+|+..|.
T Consensus       543 ~I~vl~~G~i~e~Gt  557 (575)
T PRK11160        543 QICVMDNGQIIEQGT  557 (575)
T ss_pred             EEEEEECCEEEEECC
T ss_conf             999998989999888


No 118
>pfam03397 Rhabdo_matrix Rhabdovirus matrix protein.
Probab=45.63  E-value=8.1  Score=17.57  Aligned_cols=47  Identities=23%  Similarity=0.285  Sum_probs=34.1

Q ss_pred             EEEEEEEEEECCEEEEEECCCE-----EEEECCCCCCCCCCCCCCCCHHHHH
Q ss_conf             6994114766674247645710-----0210023655333589798712552
Q gi|254780879|r  114 IIEVPTLIKDHNKDIIKKIPFA-----YARMTFATPYPKVKDHPKFDPLKIF  160 (652)
Q Consensus       114 ~~~~~~~~~~g~r~~~~~~pf~-----~~~~~l~~~~~~~~~~p~f~p~~~~  160 (652)
                      .=||+++..+|+-.|--.+|=.     ..+|.||..-......|.||||.-+
T Consensus        16 edrV~~~~teGtl~itG~~P~nl~eKi~~aMkLA~AIlggd~HPaFn~lv~l   67 (168)
T pfam03397        16 EDRVSTILTEGTLTITGPPPGNLVEKICMAMKLARAILGGDQHPAFNPLVHL   67 (168)
T ss_pred             CCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             7617999855579981789974788999999999998777777440048999


No 119
>PTZ00265 multidrug resistance protein (mdr1); Provisional
Probab=44.70  E-value=16  Score=15.48  Aligned_cols=35  Identities=23%  Similarity=0.245  Sum_probs=21.9

Q ss_pred             EEEEEHH--HHHHHHCCCCCCEEECCCEEEEECCCC--CCC
Q ss_conf             4882002--144541188997883495899841667--888
Q gi|254780879|r  555 YVSSYNH--QDAIAKNIKAGTAVKQGQIIGWIGTTG--LST  591 (652)
Q Consensus       555 y~T~YaH--lS~~a~gV~~G~~V~qGQvIG~vGsTG--~ST  591 (652)
                      +.-.|..  ...+.+++.  =+|+.||.||.||.||  -||
T Consensus      1172 V~F~Ypsrp~~pVLk~ls--f~I~~GqkVaiVGrSGsGKST 1210 (1467)
T PTZ00265       1172 VNFRYISRPNVPIYKDLS--FSCDSKKTTAIVGETGSGKST 1210 (1467)
T ss_pred             EEEECCCCCCCCCCCCEE--EEECCCCEEEEECCCCCCHHH
T ss_conf             999828999592018845--997799889998999983999


No 120
>PRK00044 psd phosphatidylserine decarboxylase; Reviewed
Probab=44.38  E-value=7  Score=18.00  Aligned_cols=21  Identities=19%  Similarity=0.460  Sum_probs=14.3

Q ss_pred             HHHCCCCCCEEECCCEEEEEC
Q ss_conf             541188997883495899841
Q gi|254780879|r  565 IAKNIKAGTAVKQGQIIGWIG  585 (652)
Q Consensus       565 ~a~gV~~G~~V~qGQvIG~vG  585 (652)
                      +...+++|++|+-||.||+.=
T Consensus       266 ~~~~l~~g~~vr~Gq~ig~~~  286 (291)
T PRK00044        266 LAEQLEAGSPTRMGEPLAHST  286 (291)
T ss_pred             CCCCCCCCCEEEECHHHCCCC
T ss_conf             032458999887165657940


No 121
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=43.99  E-value=15  Score=15.75  Aligned_cols=47  Identities=15%  Similarity=0.044  Sum_probs=24.2

Q ss_pred             ECCCCCHHHH---HHH--CCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEE
Q ss_conf             4179708999---997--4999899999999854015610169988899997
Q gi|254780879|r  281 IQHNTTIFDA---MVH--AGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGV  327 (652)
Q Consensus       281 VK~GDTL~~I---L~r--~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~  327 (652)
                      +==.||++.=   -+.  .+++.++|.+++.+-+-.-=.++|..|=...|+-
T Consensus       446 ~LFdDTiA~NvaYg~~da~~~~~a~v~~A~~~Ayl~dfvd~lP~Gldt~vG~  497 (603)
T TIGR02203       446 VLFDDTIANNVAYGRLDAEQVDRAEVERALAAAYLQDFVDKLPLGLDTPVGE  497 (603)
T ss_pred             EECCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             7205326776440423400178789999999864688871478885634241


No 122
>PRK06823 ornithine cyclodeaminase; Validated
Probab=43.66  E-value=16  Score=15.46  Aligned_cols=14  Identities=0%  Similarity=0.147  Sum_probs=5.9

Q ss_pred             CCCCHHHCCCCCEE
Q ss_conf             01561016998889
Q gi|254780879|r  310 NEVRVDQLTKDEIL  323 (652)
Q Consensus       310 ~~~~~~~Lr~Gq~L  323 (652)
                      ..++...|++|..+
T Consensus       205 Pv~~~~~lkpG~hi  218 (315)
T PRK06823        205 PLLQAEDIQPGTHI  218 (315)
T ss_pred             CCCCCCCCCCCCEE
T ss_conf             64165557899679


No 123
>PRK09282 pyruvate carboxylase subunit B; Validated
Probab=43.36  E-value=20  Score=14.83  Aligned_cols=17  Identities=29%  Similarity=0.348  Sum_probs=9.8

Q ss_pred             CCCCEEECCCCEEEEEE
Q ss_conf             96727971596799965
Q gi|254780879|r  522 RGTPIVAVGDGIVEKAN  538 (652)
Q Consensus       522 ~GTPI~Aag~G~V~~ag  538 (652)
                      .+++|-|.-.|.|++.-
T Consensus       510 ~~~~V~APmpG~V~~V~  526 (580)
T PRK09282        510 AGGPVTAPMAGNIVKVL  526 (580)
T ss_pred             CCCEECCCCCCEEEEEE
T ss_conf             99853279982699999


No 124
>PRK11892 pyruvate dehydrogenase subunit beta; Provisional
Probab=43.34  E-value=12  Score=16.47  Aligned_cols=24  Identities=13%  Similarity=0.218  Sum_probs=10.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             111222212331000134630699411
Q gi|254780879|r   93 LSSMQRARLSPKTKSKHPEKIIIEVPT  119 (652)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (652)
                      ++.-+.++...-.+   .+|-++++..
T Consensus        27 gd~v~~gd~~aeie---tdkatme~ea   50 (464)
T PRK11892         27 GDKVKSGDVIAEIE---TDKATMEVEA   50 (464)
T ss_pred             CCCCCCCCEEEEEE---ECCEEEEEEE
T ss_conf             97525786689975---0656689875


No 125
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=43.04  E-value=18  Score=15.17  Aligned_cols=35  Identities=14%  Similarity=0.202  Sum_probs=18.0

Q ss_pred             CCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHH
Q ss_conf             7279715967999653089700799983997488200214
Q gi|254780879|r  524 TPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQD  563 (652)
Q Consensus       524 TPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS  563 (652)
                      .-|+--.+|.|+..|..--     .+..++-|...|+|+.
T Consensus       551 D~Iivld~G~Ive~Gth~e-----Ll~~~g~Y~~l~~~q~  585 (588)
T PRK11174        551 DQILVMQDGKIVQQGDYAE-----LSQAQGLFATLLAHRQ  585 (588)
T ss_pred             CEEEEEECCEEEEECCHHH-----HHHCCCHHHHHHHHHH
T ss_conf             9999998988999888999-----9849997899999987


No 126
>pfam07831 PYNP_C Pyrimidine nucleoside phosphorylase C-terminal domain. This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer.
Probab=42.80  E-value=20  Score=14.77  Aligned_cols=18  Identities=33%  Similarity=0.387  Sum_probs=12.7

Q ss_pred             CCCCCEEECCCEEEEECC
Q ss_conf             889978834958998416
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGs  586 (652)
                      .+.|++|++||.|..+=+
T Consensus        38 ~k~Gd~V~~g~pl~~i~~   55 (75)
T pfam07831        38 KKVGDKVKKGDPLATIYA   55 (75)
T ss_pred             CCCCCEECCCCEEEEEEC
T ss_conf             468999669993999977


No 127
>COG4054 McrB Methyl coenzyme M reductase, beta subunit [Coenzyme metabolism]
Probab=41.91  E-value=21  Score=14.68  Aligned_cols=54  Identities=22%  Similarity=0.287  Sum_probs=34.0

Q ss_pred             CCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECC--CCCEEEEECCCCEEE
Q ss_conf             434044346420030267967279715967999653089--700799983997488
Q gi|254780879|r  504 HPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGG--YGKQTLIHHGNGYVS  557 (652)
Q Consensus       504 hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~G--yGn~V~I~H~~Gy~T  557 (652)
                      +-||-|-.---||||.-..||-|==.-=---+|-|-..|  .||.|+-||..|+--
T Consensus       339 NDilEyETGLPgvDfGraeGtAVGFSFFSHSIYGGGGPGiF~GNHvVTRHSkGFAi  394 (447)
T COG4054         339 NDILEYETGLPGVDFGRAEGTAVGFSFFSHSIYGGGGPGIFNGNHVVTRHSKGFAI  394 (447)
T ss_pred             HHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCCEEEEECCCCCCC
T ss_conf             44666623998765454343275556432100058988640486467743677544


No 128
>pfam01887 SAM_adeno_trans S-adenosyl-l-methionine hydroxide adenosyltransferase. This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme. S-adenosyl-l-methionine hydroxide adenosyltransferases utilizes a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. This family used to be known as DUF62.
Probab=41.71  E-value=21  Score=14.66  Aligned_cols=22  Identities=27%  Similarity=0.696  Sum_probs=14.6

Q ss_pred             EECCCEEEEECCCCCCCCCEEEEEEEECC
Q ss_conf             83495899841667888742688997867
Q gi|254780879|r  575 VKQGQIIGWIGTTGLSTGPHLHYELIVNG  603 (652)
Q Consensus       575 V~qGQvIG~vGsTG~STGPHLHfEv~vnG  603 (652)
                      |..|+...|.||.|       +.||-+|.
T Consensus       220 v~~G~~~~~~~S~G-------~lEIavn~  241 (258)
T pfam01887       220 VPPGELLAYVNSSG-------FLEIAVNQ  241 (258)
T ss_pred             CCCCCEEEEECCCC-------CEEEEECC
T ss_conf             79998899998999-------19999817


No 129
>cd06849 lipoyl_domain Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3) and play a key role in redox regulation. E2, the central component of the complex, catalyzes the transfer of the acyl group of CoA from E1 to E3 via reductive acetylation of a lipoyl group covalently attached to a lysine residue.
Probab=41.66  E-value=20  Score=14.78  Aligned_cols=29  Identities=24%  Similarity=0.325  Sum_probs=16.6

Q ss_pred             EEEEHHHHHHHH--CCCCCCEEECCCEEEEE
Q ss_conf             882002144541--18899788349589984
Q gi|254780879|r  556 VSSYNHQDAIAK--NIKAGTAVKQGQIIGWI  584 (652)
Q Consensus       556 ~T~YaHlS~~a~--gV~~G~~V~qGQvIG~v  584 (652)
                      ...++..+....  -+++|+.|+.||+|+++
T Consensus        44 ~~i~a~~~G~v~~i~~~~G~~v~~G~~l~~i   74 (74)
T cd06849          44 VEVEAPAAGVLAKILVEEGDTVPVGQVIAVI   74 (74)
T ss_pred             EEEECCCCEEEEEEEECCCCEECCCCEEEEC
T ss_conf             8410798999999987899998899999979


No 130
>PRK10125 predicted glycosyl transferase; Provisional
Probab=41.36  E-value=10  Score=16.88  Aligned_cols=40  Identities=18%  Similarity=0.239  Sum_probs=24.9

Q ss_pred             CCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCC
Q ss_conf             267967279715967999653089700799983997488200214454118
Q gi|254780879|r  519 AAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNI  569 (652)
Q Consensus       519 aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV  569 (652)
                      |-.+||||+|-..|=+-           -+|+|.|||+-.|.--..++.++
T Consensus       326 a~acg~pvv~~~~~g~~-----------~~~~~~~g~~~~~~d~~~la~~i  365 (405)
T PRK10125        326 ALSIGVPVIATHSDAAR-----------EVLQKSGGKTVSEEEVLQLAQLS  365 (405)
T ss_pred             HHHCCCCEEEECCCCCH-----------HHEECCCCEEECCCCHHHHHHHH
T ss_conf             99749988983599973-----------65115874596688999999989


No 131
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The  N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide.  The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=40.34  E-value=17  Score=15.23  Aligned_cols=48  Identities=19%  Similarity=0.236  Sum_probs=24.7

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEE
Q ss_conf             96799965308970079998399748820021445411---8899788349589
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQII  581 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvI  581 (652)
                      .|+|...   --||=+|.|.+.++-..--.|.|.++..   -.+.+-++.||.|
T Consensus         5 ~G~V~~i---~~fGaFV~l~~~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V   55 (79)
T cd05684           5 KGKVTSI---MDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKV   55 (79)
T ss_pred             EEEEEEE---EEEEEEEEEECCCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEE
T ss_conf             9999899---75339999967889806789956815755558988936799999


No 132
>COG4656 RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion]
Probab=40.19  E-value=14  Score=15.88  Aligned_cols=23  Identities=13%  Similarity=0.094  Sum_probs=11.5

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHH
Q ss_conf             68841797089999974999899
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGD  300 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~e  300 (652)
                      .+.|+=|..+..+|...|.-..+
T Consensus       299 nv~VrIGTP~~~lL~~~G~~~~~  321 (529)
T COG4656         299 NVWVRIGTPVSQLLNEAGGIDTK  321 (529)
T ss_pred             EEEEECCCCHHHHHHHCCCCCCC
T ss_conf             08997789499999974897678


No 133
>TIGR01924 rsbW_low_gc anti-sigma B factor; InterPro: IPR010193   This entry describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter . RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex . Low ATP level or environmental stress causes the dephosphorylation of RsbV .; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0045892 negative regulation of transcription DNA-dependent.
Probab=39.89  E-value=15  Score=15.60  Aligned_cols=60  Identities=15%  Similarity=0.305  Sum_probs=32.2

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCC-CCEEEEEEECCCCCEEEEE
Q ss_conf             708999997499989999999985401561016998889999727888-6405899971688348999
Q gi|254780879|r  285 TTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDD-KFTIVRFSIYHKQKHLLTI  351 (652)
Q Consensus       285 DTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~-~~~~~r~si~~~~~~~~~v  351 (652)
                      =||+.|+.|.|+++++|.-+==|.+... .+..      .=.+....+ ..--+++.+|.+.....+.
T Consensus        25 LtlSGvasR~GytYd~IED~KIAVSEA~-TN~V------~HAYke~~nvG~~~i~F~iyEDklev~vs   85 (161)
T TIGR01924        25 LTLSGVASRAGYTYDDIEDLKIAVSEAC-TNAV------KHAYKEEENVGEISIEFEIYEDKLEVIVS   85 (161)
T ss_pred             EEEHHHHHHCCCCHHHHHHHHHHHHHHH-CCCE------EEEECCCCCEEEEEEEEEEEEEEEEEEEE
T ss_conf             4102565524878657520677665553-0331------12230898367899888788757899982


No 134
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=39.72  E-value=22  Score=14.45  Aligned_cols=15  Identities=20%  Similarity=0.435  Sum_probs=8.8

Q ss_pred             CCCCCEEECCCEEEE
Q ss_conf             889978834958998
Q gi|254780879|r  569 IKAGTAVKQGQIIGW  583 (652)
Q Consensus       569 V~~G~~V~qGQvIG~  583 (652)
                      +++|+.|..||++..
T Consensus        54 v~~Gd~V~~G~~L~~   68 (70)
T PRK08225         54 VQEGDFVNEGDVLLE   68 (70)
T ss_pred             ECCCCEECCCCEEEE
T ss_conf             589899899999999


No 135
>TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Probab=38.97  E-value=23  Score=14.37  Aligned_cols=43  Identities=16%  Similarity=0.094  Sum_probs=28.3

Q ss_pred             CCHHHHHHHCC----CCHHHHHHHHHHHHC----CCCHHHCCCCCEEEEEE
Q ss_conf             70899999749----998999999998540----15610169988899997
Q gi|254780879|r  285 TTIFDAMVHAG----YSNGDSAKIAKALKN----EVRVDQLTKDEILRIGV  327 (652)
Q Consensus       285 DTL~~IL~r~G----vs~~ei~~i~~al~~----~~~~~~Lr~Gq~L~I~~  327 (652)
                      |||++|+.++-    ++..+++-.+...|.    ..+.+.|+.|..|+++.
T Consensus         1 dTLw~IA~~~~~~~~~s~~Q~M~ai~~~Np~AF~~~niN~L~~g~~L~iP~   51 (74)
T TIGR03505         1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPS   51 (74)
T ss_pred             CCHHHHHHHHCCCCCCCHHHHHHHHHHHCHHHHHCCCHHHHCCCCEEECCC
T ss_conf             958999998776889899999999999895977348831323799555859


No 136
>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=38.86  E-value=20  Score=14.77  Aligned_cols=15  Identities=13%  Similarity=0.155  Sum_probs=9.1

Q ss_pred             CEEECCCCEEEEEEE
Q ss_conf             279715967999653
Q gi|254780879|r  525 PIVAVGDGIVEKANW  539 (652)
Q Consensus       525 PI~Aag~G~V~~ag~  539 (652)
                      -|+=-.+|.|+..|.
T Consensus       543 ~I~vl~~G~ive~Gt  557 (593)
T PRK10790        543 TILVLHRGQAVEQGT  557 (593)
T ss_pred             EEEEEECCEEEEECC
T ss_conf             999998999999727


No 137
>COG0845 AcrA Membrane-fusion protein [Cell envelope biogenesis, outer membrane]
Probab=38.48  E-value=23  Score=14.32  Aligned_cols=12  Identities=17%  Similarity=-0.050  Sum_probs=4.2

Q ss_pred             CCCEEEEECCCC
Q ss_conf             495899841667
Q gi|254780879|r  577 QGQIIGWIGTTG  588 (652)
Q Consensus       577 qGQvIG~vGsTG  588 (652)
                      .|+.|---|.++
T Consensus       347 ~G~~v~v~~~~~  358 (372)
T COG0845         347 PGDRVVVEGLFL  358 (372)
T ss_pred             CCCEEEEECCCC
T ss_conf             998999953223


No 138
>COG0213 DeoA Thymidine phosphorylase [Nucleotide transport and metabolism]
Probab=37.91  E-value=24  Score=14.26  Aligned_cols=57  Identities=30%  Similarity=0.337  Sum_probs=40.5

Q ss_pred             CCCCCCEEECCCCEEEEE--------EEECCCCCEEE---EECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC
Q ss_conf             679672797159679996--------53089700799---98399748820021445411889978834958998416
Q gi|254780879|r  520 APRGTPIVAVGDGIVEKA--------NWAGGYGKQTL---IHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       520 Ap~GTPI~Aag~G~V~~a--------g~~~GyGn~V~---I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs  586 (652)
                      ++.=-+|+|.-+|.|.+.        .+.=|.|+.+.   |+|+-|..   .|       .|.|++|+.|+.|..+=+
T Consensus       333 ~~~~~~v~A~~~G~v~~id~~~ig~~a~~lGAgR~~k~d~iD~~aGi~---l~-------kk~ge~Vk~Gd~l~tiya  400 (435)
T COG0213         333 AKYTAEVKAQTSGYVSEIDARAIGMAAMELGAGRATKTDRIDKGAGIY---LH-------KKLGEKVKKGDPLATIYA  400 (435)
T ss_pred             CCEEEEEECCCCEEEEEECHHHHHHHHHHHCCCCCCCCCCCCCCCCEE---EE-------ECCCCEECCCCEEEEEEC
T ss_conf             765888864676268762558999999980899788734347556669---98-------317983026974799862


No 139
>pfam09449 DUF2020 Domain of unknown function (DUF2020). Protein of unknown function found in bacteria.
Probab=37.60  E-value=24  Score=14.23  Aligned_cols=24  Identities=50%  Similarity=0.822  Sum_probs=10.8

Q ss_pred             CEEECCCCCCCEEECCCCEEEEEEEECCC
Q ss_conf             00302679672797159679996530897
Q gi|254780879|r  515 GVDWAAPRGTPIVAVGDGIVEKANWAGGY  543 (652)
Q Consensus       515 GVD~aAp~GTPI~Aag~G~V~~ag~~~Gy  543 (652)
                      =|||+||+-+-=.|.     ...||.||+
T Consensus        76 vVd~aAPid~t~pa~-----eP~GWsGGr   99 (144)
T pfam09449        76 VVDWAAPIDSTEPAE-----EPAGWSGGR   99 (144)
T ss_pred             HHCCCCCCCCCCCCC-----CCCCCCCCC
T ss_conf             734457645568476-----887753653


No 140
>COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=37.47  E-value=16  Score=15.46  Aligned_cols=11  Identities=9%  Similarity=0.184  Sum_probs=5.2

Q ss_pred             EEECCCCCHHH
Q ss_conf             88417970899
Q gi|254780879|r  279 IPIQHNTTIFD  289 (652)
Q Consensus       279 v~VK~GDTL~~  289 (652)
                      ..|+.|||+.-
T Consensus        31 L~v~~Ge~vai   41 (228)
T COG4181          31 LVVKRGETVAI   41 (228)
T ss_pred             EEECCCCEEEE
T ss_conf             78627865888


No 141
>TIGR01711 gspJ general secretion pathway protein J; InterPro: IPR010055   This entry represents GspJ, one of two proteins highly conserved at their N-termini and described by Bacterial type II secretion system protein I/J but is easily separable phylogenetically. The other is the General secretion pathway protein I. Both GspI and GspJ are proteins of the type II secretion pathway, or main terminal branch of the general secretion pathway. This pathway carries proteins across the outer membrane. Note that proteins of type II secretion are cryptic in Escherichia coli K-12 - present but not yet demonstrated to act on any target.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=37.29  E-value=20  Score=14.83  Aligned_cols=16  Identities=25%  Similarity=0.302  Sum_probs=7.0

Q ss_pred             CCCCEEEEEEECCCCC
Q ss_conf             4672368896238854
Q gi|254780879|r  442 DDSELLYIHARFGETR  457 (652)
Q Consensus       442 ~~geil~A~~~~~g~~  457 (652)
                      ..+++..+.....++.
T Consensus       106 pRs~lqrVgwrL~~~~  121 (202)
T TIGR01711       106 PRSELQRVGWRLKDEK  121 (202)
T ss_pred             CCCCEEEEEEEECCCE
T ss_conf             7421235444514772


No 142
>KOG2525 consensus
Probab=36.90  E-value=25  Score=14.15  Aligned_cols=23  Identities=9%  Similarity=0.122  Sum_probs=16.1

Q ss_pred             CCEEECCCCCCCEEECCCCEEEE
Q ss_conf             20030267967279715967999
Q gi|254780879|r  514 TGVDWAAPRGTPIVAVGDGIVEK  536 (652)
Q Consensus       514 ~GVD~aAp~GTPI~Aag~G~V~~  536 (652)
                      .|++|..-.++|=+...+.+...
T Consensus       394 ~~~~F~~Vvf~Pni~~~~~~~~~  416 (496)
T KOG2525         394 IGTRFSSVVFMPNITSSSPVGSA  416 (496)
T ss_pred             CCCCCCEEEECCCCCCCCCCCCH
T ss_conf             34451417852443115876664


No 143
>PRK05559 DNA topoisomerase IV subunit B; Reviewed
Probab=36.78  E-value=25  Score=14.14  Aligned_cols=11  Identities=9%  Similarity=0.299  Sum_probs=5.3

Q ss_pred             HHHHHHHHCCC
Q ss_conf             99999984147
Q gi|254780879|r  632 KRINSLLNNGE  642 (652)
Q Consensus       632 ~~id~ll~~~~  642 (652)
                      +.++.||.+..
T Consensus       607 ~~~~~lmg~~~  617 (633)
T PRK05559        607 ELVDMLMGKKA  617 (633)
T ss_pred             HHHHHHHCCCC
T ss_conf             99999828995


No 144
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=36.64  E-value=7.6  Score=17.74  Aligned_cols=49  Identities=12%  Similarity=0.188  Sum_probs=27.8

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHHHHHHHH--HCCCCHHHCCCCCEEEEE
Q ss_conf             6884179708999997499989999999985--401561016998889999
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKAL--KNEVRVDQLTKDEILRIG  326 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al--~~~~~~~~Lr~Gq~L~I~  326 (652)
                      ...+..|.|+.++|..+++.+.-+.++...+  +.......|+.|+++.|.
T Consensus         9 ~~~lp~g~tvadll~~l~~~~~~AVavN~~~VPRs~~~~~~L~~GD~ieiv   59 (65)
T PRK06944          9 TLSLPDGATVADALAAYGARPPFAVAVNGNFVARTQHAARALAAGDRLDLV   59 (65)
T ss_pred             EEECCCCCCHHHHHHHCCCCCCEEEEECCEEECHHHHHHCCCCCCCEEEEE
T ss_conf             642799997999998628689779998479803145333127899999999


No 145
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=36.53  E-value=22  Score=14.50  Aligned_cols=25  Identities=16%  Similarity=0.321  Sum_probs=14.8

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHHHC
Q ss_conf             0899999749998999999998540
Q gi|254780879|r  286 TIFDAMVHAGYSNGDSAKIAKALKN  310 (652)
Q Consensus       286 TL~~IL~r~Gvs~~ei~~i~~al~~  310 (652)
                      .|..-|.+.|++..=+..++..+..
T Consensus       294 ~L~krL~~~GfS~~Lar~L~~~lP~  318 (557)
T PRK12727        294 QALELMDDYGFDAGLTRDVAMQIPA  318 (557)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf             9999999766999999999974833


No 146
>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional
Probab=36.00  E-value=25  Score=14.06  Aligned_cols=52  Identities=8%  Similarity=0.035  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCC
Q ss_conf             223342226654456777764013688417970899999749998999999998540156
Q gi|254780879|r  254 IIEENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVR  313 (652)
Q Consensus       254 ~~~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~  313 (652)
                      +.=+||++.-+..    .+...+-...|++|++++- .-..|--...+.++   +.+.++
T Consensus       335 I~~~~VsF~Y~~~----~~vL~~isl~i~~Ge~vai-VG~SGsGKSTL~~L---L~gly~  386 (585)
T PRK13657        335 VEFDDVSFSYDNS----RQAVEDVSFEAKPGQTVAI-VGPTGAGKSTLINL---LHRVFD  386 (585)
T ss_pred             EEEEEEEEECCCC----CCCCCCCEEEECCCCEEEE-ECCCCCCHHHHHHH---HHHHCC
T ss_conf             9999879867999----8753670389759988999-88989869999999---860157


No 147
>smart00566 consensus
Probab=35.95  E-value=25  Score=14.11  Aligned_cols=11  Identities=64%  Similarity=1.159  Sum_probs=8.2

Q ss_pred             CEEEEEEEECC
Q ss_conf             42688997867
Q gi|254780879|r  593 PHLHYELIVNG  603 (652)
Q Consensus       593 PHLHfEv~vnG  603 (652)
                      .+|||+|..||
T Consensus        79 ~slhy~~~~~G   89 (90)
T smart00566       79 GSLHYQLLVNG   89 (90)
T ss_pred             CCEEEEEEEEC
T ss_conf             94999999704


No 148
>PTZ00243 ABC transporter; Provisional
Probab=35.88  E-value=26  Score=14.04  Aligned_cols=53  Identities=23%  Similarity=0.304  Sum_probs=29.6

Q ss_pred             CEEEEEH-HHHHHHHCCCCCCEEECCCEEEEECCCCC--CCCCEEE--------EEEEECCEECCC
Q ss_conf             7488200-21445411889978834958998416678--8874268--------899786788366
Q gi|254780879|r  554 GYVSSYN-HQDAIAKNIKAGTAVKQGQIIGWIGTTGL--STGPHLH--------YELIVNGIKVDS  608 (652)
Q Consensus       554 Gy~T~Ya-HlS~~a~gV~~G~~V~qGQvIG~vGsTG~--STGPHLH--------fEv~vnG~~VdP  608 (652)
                      ++...|. ++.-..++|.  =+|+.||.||-||-||-  ||=-.+=        =.|.++|.-+.=
T Consensus      1313 nVs~rYr~~lp~VLk~Is--f~I~pGEKVGIVGRTGSGKSSLi~aLfRl~e~~~G~I~IDGvDIs~ 1376 (1560)
T PTZ00243       1313 GVQMRYREGLPLVLRGVS--FRIAPREKVGIVGRTGSGKSTLLLTFMRMVEVCGGEIRVNGREIGA 1376 (1560)
T ss_pred             EEEEECCCCCCCCCCCEE--EEECCCCEEEEECCCCCHHHHHHHHHHCCCCCCCCEEEECCEEHHH
T ss_conf             889972899987105746--9988999999987987439999999970327788989997998202


No 149
>PRK01734 consensus
Probab=35.49  E-value=14  Score=15.94  Aligned_cols=34  Identities=6%  Similarity=-0.015  Sum_probs=18.5

Q ss_pred             HHHHHHCCCCHHHHHHH-H---HHHHCCCCHHHCCCCCE
Q ss_conf             99999749998999999-9---98540156101699888
Q gi|254780879|r  288 FDAMVHAGYSNGDSAKI-A---KALKNEVRVDQLTKDEI  322 (652)
Q Consensus       288 ~~IL~r~Gvs~~ei~~i-~---~al~~~~~~~~Lr~Gq~  322 (652)
                      ..-.+.|+++-+|+..= .   .+|+..+ .++|++|-+
T Consensus        49 ~~fik~y~inl~Ea~~~~~~~Y~sfn~FF-tR~LKp~aR   86 (294)
T PRK01734         49 KAFAKKYNVDMSEAQKENFSDYASFNEFF-IRPLKENAR   86 (294)
T ss_pred             HHHHHHHCCCHHHHCCCCHHHCCCHHHHE-ECCCCCCCC
T ss_conf             99999979897897469812168789928-111666665


No 150
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=35.26  E-value=26  Score=13.98  Aligned_cols=57  Identities=30%  Similarity=0.376  Sum_probs=41.1

Q ss_pred             CCCCCEEEEECCCCEEEEEHHHHHHHHC---CCCCCEEECCCEEEEECCCCCCCCCEEEEEEEECCEECCCCEE
Q ss_conf             8970079998399748820021445411---8899788349589984166788874268899786788366200
Q gi|254780879|r  541 GGYGKQTLIHHGNGYVSSYNHQDAIAKN---IKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKV  611 (652)
Q Consensus       541 ~GyGn~V~I~H~~Gy~T~YaHlS~~a~g---V~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~  611 (652)
                      ++--|-|.|...+|-.|.|+-+.-=-+|   |.+|++|=+|++||.--              |-|---|||+|-
T Consensus       480 ~~R~nGvLiS~~~G~a~~yal~~lqdRG~~Fi~pG~~vYeGmiiG~hs--------------R~nDL~VN~~k~  539 (603)
T COG1217         480 GGRHNGVLISNETGKAVAYALFNLQDRGKLFIEPGTKVYEGMIIGEHS--------------RDNDLTVNVLKG  539 (603)
T ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHCCCEEECCCCCEEEEEEEEEEC--------------CCCCCEECCCCC
T ss_conf             555451599768984347655358753756645997265016985306--------------756713424234


No 151
>pfam11545 HemeBinding_Shp Cell surface heme-binding protein Shp. Shp is part of a complex which functions in heme uptake in Streptococcus pyogenes. During which, Shp transfers its heme to HtsA which is a component of an ABC transporter. The heme binding region of Shp contains an immunoglobulin-like beta-sandwich fold and has a unique heme-iron coordination with the axial ligands being two methionine residues from the same Shp molecule. Surrounding the heme pocket, there is a negative surface which may serve as a docking interface for heme transfer.
Probab=34.87  E-value=26  Score=13.94  Aligned_cols=97  Identities=18%  Similarity=0.236  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEE-ECCCCEEEEEHHHHHHHHCCCCCCEEECC-
Q ss_conf             6414340443464200302679672797159679996530897007999-83997488200214454118899788349-
Q gi|254780879|r  501 MRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLI-HHGNGYVSSYNHQDAIAKNIKAGTAVKQG-  578 (652)
Q Consensus       501 ~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I-~H~~Gy~T~YaHlS~~a~gV~~G~~V~qG-  578 (652)
                      ..+||+.|..        .-+-|++-+|.|.|-|+-+=|..+   +++. +-+.-|.|.=.||-.+.++++  -||..+ 
T Consensus        13 sY~hPvTG~i--------ED~Gg~~~~aiGqgMVe~~V~s~~---llE~td~Gk~YlTvr~~L~d~~sn~~--f~VQ~~g   79 (151)
T pfam11545        13 NYRHPVSGQI--------EDSGGEHSFDIGQGMVEGTVYSDG---MLEVTDAGKIYLTFRMSLADYSGNYQ--FWVQPGG   79 (151)
T ss_pred             CCCCCCCCEE--------ECCCCCCCCCHHHHHHHHEECCCE---EEEECCCCCEEEEEEEEEHHCCCCCE--EEEEECC
T ss_conf             5458775357--------348987562111123121441541---69981799789999976201267835--9998789


Q ss_pred             ------CEEEEECCCCCCCCCEEEEEEEECC--------EECCCCE
Q ss_conf             ------5899841667888742688997867--------8836620
Q gi|254780879|r  579 ------QIIGWIGTTGLSTGPHLHYELIVNG--------IKVDSTK  610 (652)
Q Consensus       579 ------QvIG~vGsTG~STGPHLHfEv~vnG--------~~VdP~~  610 (652)
                            .-+...|+.-...|--.||.|-++.        -+|.||-
T Consensus        80 dg~f~~va~t~T~~g~d~ngtt~D~ri~vps~n~vvr~smYVePMG  125 (151)
T pfam11545        80 TGSFQAVAYNITQKGTDTNGTTLDIAISLPTVNSVVRGSMYVEPMG  125 (151)
T ss_pred             CCCEEEEEEEEECCCCCCCCCEEEEEEECCCCCCEEEEEEEECCCC
T ss_conf             8960350067620130279965779996288881898999982489


No 152
>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2.  A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.
Probab=34.66  E-value=27  Score=13.91  Aligned_cols=24  Identities=8%  Similarity=0.124  Sum_probs=9.1

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHH
Q ss_conf             6884179708999997499989999
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSA  302 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~  302 (652)
                      ...|++|+.+. |.-..|--...+.
T Consensus        24 sl~i~~G~~v~-ivG~sGsGKSTLl   47 (220)
T cd03245          24 SLTIRAGEKVA-IIGRVGSGKSTLL   47 (220)
T ss_pred             EEEECCCCEEE-EECCCCCHHHHHH
T ss_conf             99987999999-9999998599999


No 153
>COG1156 NtpB Archaeal/vacuolar-type H+-ATPase subunit B [Energy production and conversion]
Probab=34.22  E-value=27  Score=13.87  Aligned_cols=29  Identities=14%  Similarity=-0.003  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             34444445565033443202333222456
Q gi|254780879|r  195 ITRIQLDHTAQDEEIKNAIMNQFFLLHNK  223 (652)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (652)
                      ..+.-..+.+...+...+++.+..+..+.
T Consensus       148 KlPIFSgSGlphN~LaaqIarQA~v~~~~  176 (463)
T COG1156         148 KLPIFSGSGLPHNELAAQIARQATVDGEE  176 (463)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCCCCCC
T ss_conf             46601279984379999999753667875


No 154
>COG0508 AceF Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes [Energy production and conversion]
Probab=33.76  E-value=26  Score=14.02  Aligned_cols=14  Identities=21%  Similarity=0.389  Sum_probs=7.2

Q ss_pred             CCCCCHHHHHHHHH
Q ss_conf             78788899999999
Q gi|254780879|r  616 RENLKGDLLQRFAM  629 (652)
Q Consensus       616 ~~~l~~~~l~~F~~  629 (652)
                      .|.++|.+-+.|..
T Consensus       376 HRviDGa~a~~Fl~  389 (404)
T COG0508         376 HRVIDGAEAARFLV  389 (404)
T ss_pred             CCCCCCHHHHHHHH
T ss_conf             63327387889999


No 155
>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1.  In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD.  MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
Probab=33.61  E-value=28  Score=13.80  Aligned_cols=14  Identities=21%  Similarity=0.299  Sum_probs=6.6

Q ss_pred             CEEECCCCEEEEEE
Q ss_conf             27971596799965
Q gi|254780879|r  525 PIVAVGDGIVEKAN  538 (652)
Q Consensus       525 PI~Aag~G~V~~ag  538 (652)
                      -|+--.+|.|+..|
T Consensus       206 ~Iivl~~G~Ive~G  219 (238)
T cd03249         206 LIAVLQNGQVVEQG  219 (238)
T ss_pred             EEEEEECCEEEEEC
T ss_conf             99999899999988


No 156
>COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]
Probab=33.51  E-value=19  Score=14.92  Aligned_cols=17  Identities=18%  Similarity=0.290  Sum_probs=8.4

Q ss_pred             HHHHCCCCCCCCCCCCC
Q ss_conf             87626884100486200
Q gi|254780879|r   62 LTALDGHQKIAIPAKLS   78 (652)
Q Consensus        62 ~~aldg~~~~a~p~~~~   78 (652)
                      +.||+|+.-..+++.+.
T Consensus        28 ~Vallg~ey~gmrp~mk   44 (447)
T COG1726          28 EVALLGEEYVGMRPSMK   44 (447)
T ss_pred             EEEECCCCCCCCCCCCE
T ss_conf             79871651468887415


No 157
>TIGR00062 L27 ribosomal protein L27; InterPro: IPR001684   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=33.36  E-value=28  Score=13.77  Aligned_cols=30  Identities=17%  Similarity=0.325  Sum_probs=25.8

Q ss_pred             CCCCCCEEECCCCCCCEEECCCCEEEEEEE
Q ss_conf             346420030267967279715967999653
Q gi|254780879|r  510 SRMHTGVDWAAPRGTPIVAVGDGIVEKANW  539 (652)
Q Consensus       510 ~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~  539 (652)
                      .++|.|-..+.-.-.-|+|..||+|.|.-.
T Consensus        43 Tk~~~G~NVg~G~D~tlFA~~~G~V~f~~~   72 (83)
T TIGR00062        43 TKFYPGENVGLGKDDTLFALSDGVVKFEKK   72 (83)
T ss_pred             CEEECCCEEECCCCCEEEECCCCEEEEEEC
T ss_conf             652178500037885366515885876345


No 158
>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export.  They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins.  The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities.  The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=33.20  E-value=28  Score=13.75  Aligned_cols=29  Identities=14%  Similarity=0.189  Sum_probs=14.5

Q ss_pred             CEEEEEECCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             013688417970899999749998999999
Q gi|254780879|r  275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKI  304 (652)
Q Consensus       275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i  304 (652)
                      ..-...|++|+.+ .|.-+.|.-.....++
T Consensus        19 ~~isl~i~~Ge~i-~ivG~sGsGKSTLl~l   47 (171)
T cd03228          19 KDVSLTIKPGEKV-AIVGPSGSGKSTLLKL   47 (171)
T ss_pred             ECEEEEECCCCEE-EEECCCCCHHHHHHHH
T ss_conf             7718998599899-9999999839999999


No 159
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein; InterPro: IPR010068   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This entry identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulphonates, and sulphate esters import sulphur when sulphate levels are low. The most closely related proteins outside this family are putative aliphatic sulphonate binding proteins..
Probab=32.69  E-value=9.7  Score=17.01  Aligned_cols=13  Identities=31%  Similarity=0.519  Sum_probs=6.5

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             9989999999973
Q gi|254780879|r  399 MNSNLVKLIMRTL  411 (652)
Q Consensus       399 ip~~ii~~lv~i~  411 (652)
                      .++.++.+|++..
T Consensus       198 knPe~v~aF~Kv~  210 (304)
T TIGR01729       198 KNPEVVKAFVKVL  210 (304)
T ss_pred             HCHHHHHHHHHHH
T ss_conf             0707899999889


No 160
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=32.62  E-value=29  Score=13.69  Aligned_cols=17  Identities=29%  Similarity=0.421  Sum_probs=12.5

Q ss_pred             CCCCCEEECCCEEEEEC
Q ss_conf             88997883495899841
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIG  585 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vG  585 (652)
                      +++|+.|..||++-.+|
T Consensus       116 v~~G~~V~~g~~L~~ig  132 (132)
T PRK06549        116 VGPGQVVNPGDGLITIG  132 (132)
T ss_pred             ECCCCEECCCCEEEEEC
T ss_conf             47989989999899949


No 161
>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional
Probab=32.47  E-value=29  Score=13.67  Aligned_cols=12  Identities=8%  Similarity=0.191  Sum_probs=5.2

Q ss_pred             CCEEECCCCEEE
Q ss_conf             727971596799
Q gi|254780879|r  524 TPIVAVGDGIVE  535 (652)
Q Consensus       524 TPI~Aag~G~V~  535 (652)
                      .-|+.--||.|+
T Consensus       214 drvi~l~~G~Iv  225 (228)
T PRK10584        214 DRRLRLVNGQLQ  225 (228)
T ss_pred             CCEEEEECCEEE
T ss_conf             979999899999


No 162
>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=32.38  E-value=20  Score=14.79  Aligned_cols=25  Identities=16%  Similarity=0.142  Sum_probs=12.8

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHHH
Q ss_conf             68841797089999974999899999
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSAK  303 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~  303 (652)
                      ...+|+||-+.-| -.+|-.......
T Consensus       343 Nl~ikrGelvFli-G~NGsGKST~~~  367 (546)
T COG4615         343 NLTIKRGELVFLI-GGNGSGKSTLAM  367 (546)
T ss_pred             EEEEECCCEEEEE-CCCCCCHHHHHH
T ss_conf             3687337389998-889963889999


No 163
>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=32.11  E-value=27  Score=13.92  Aligned_cols=22  Identities=14%  Similarity=0.225  Sum_probs=7.8

Q ss_pred             ECCCCCHHHHHHHCCCCHHHHHH
Q ss_conf             41797089999974999899999
Q gi|254780879|r  281 IQHNTTIFDAMVHAGYSNGDSAK  303 (652)
Q Consensus       281 VK~GDTL~~IL~r~Gvs~~ei~~  303 (652)
                      |++|+.+ .|+-.+|.-.....+
T Consensus        22 v~~GEiv-~ilGpNGaGKSTllk   43 (177)
T cd03222          22 VKEGEVI-GIVGPNGTGKTTAVK   43 (177)
T ss_pred             CCCCCEE-EEECCCCCCHHHHHH
T ss_conf             5899899-998999999999999


No 164
>TIGR01474 ubiA_proteo 4-hydroxybenzoate polyprenyl transferase; InterPro: IPR006370   These sequences are a family of integral membrane proteins that condense para-hydroxybenzoate with any of several polyprenyldiphosphates. Heterologous expression studies suggest that for, many but not all members, the activity seen (e.g. octaprenyltransferase in Escherichia coli) reflects available host isoprenyl pools rather than enzyme specificity. A fairly deep split by both clustering (UPGMA) and phylogenetics (NJ tree) separates this group (mostly Proteobacterial and mitochondrial), with several characterised members, from another group (mostly archaeal and Gram-positive bacterial) lacking characterised members IPR006371 from INTERPRO .; GO: 0004659 prenyltransferase activity, 0009058 biosynthetic process, 0016021 integral to membrane.
Probab=31.57  E-value=6.9  Score=18.07  Aligned_cols=17  Identities=24%  Similarity=0.112  Sum_probs=10.0

Q ss_pred             CCCCCCCCCCCCCEEEHH
Q ss_conf             476544578854113189
Q gi|254780879|r   24 GNNDAKIFLDNRRKVSLR   41 (652)
Q Consensus        24 ~~~~~~~~~~~rr~vs~r   41 (652)
                      |++.+.++++ =++||.|
T Consensus        74 VeRTk~RPLa-sG~vs~~   90 (291)
T TIGR01474        74 VERTKSRPLA-SGAVSVR   90 (291)
T ss_pred             CCCCCCCCCC-CCCCHHH
T ss_conf             4000037874-6631189


No 165
>TIGR01381 E1_like_apg7 E1-like protein-activating enzyme Gsa7p/Apg7p; InterPro: IPR006285   This is a family of eukaryotic proteins found in animals, plants, and yeasts that includes Apg7p (YHR171W) from Saccharomyces cerevisiae and GSA7 from Pichia pastoris. Members are about 650 to 700 residues in length and include a central domain of about 150 residues shared with the ThiF/MoeB/HesA family of proteins. A low level of similarity to ubiquitin-activating enzyme E1 is described in a paper on peroxisome autophagy mediated by GSA7, and is the basis of the name ubiquitin activating enzyme E1-like protein. Members of the family appear to be involved in protein lipidation events analogous to ubiquitination and required for membrane fusion events during autophagy. .
Probab=31.44  E-value=28  Score=13.81  Aligned_cols=119  Identities=18%  Similarity=0.191  Sum_probs=58.6

Q ss_pred             CCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCC----------
Q ss_conf             1246723688962388542013455766554443355661000001123334541023567641434044----------
Q gi|254780879|r  440 ASDDSELLYIHARFGETRTRFYRFLNPVDGSVEYFNENGKSSRPFLLRTPVPFGRMTSGFGMRYHPILGY----------  509 (652)
Q Consensus       440 ~~~~geil~A~~~~~g~~~~~yrf~~~~~~~~~yyd~~G~S~~k~llr~Pv~~~risS~Fg~R~hPilg~----------  509 (652)
                      ++++|++-|-....    -..|.|++--.+...-...-.+++++-|.-.-..+-++.=  -|--|||.-.          
T Consensus       377 FvDngkVs~sNPVR----QsL~nFeDcl~gG~~KAetA~kalk~IFP~i~~~g~~l~v--PMpGHpi~~~~~~~~~~D~~  450 (689)
T TIGR01381       377 FVDNGKVSYSNPVR----QSLYNFEDCLEGGEGKAETAAKALKRIFPAIEASGYRLEV--PMPGHPIDEKDVDELLEDIK  450 (689)
T ss_pred             EEECCEEEECCCCC----CCCCCHHHHHCCCCHHHHHHHHHHHHHCHHHHCCCEEEEE--CCCCCCCCCCCHHHHHHHHH
T ss_conf             86457454027746----8764336451378623899999998625002015317861--68888887221266899999


Q ss_pred             -----CCCCCCE----EECCCCCCC-EEECCCCEEEEEEEECCCCCEEEEECCCC-EEEEEHHHHHH
Q ss_conf             -----3464200----302679672-79715967999653089700799983997-48820021445
Q gi|254780879|r  510 -----SRMHTGV----DWAAPRGTP-IVAVGDGIVEKANWAGGYGKQTLIHHGNG-YVSSYNHQDAI  565 (652)
Q Consensus       510 -----~r~H~GV----D~aAp~GTP-I~Aag~G~V~~ag~~~GyGn~V~I~H~~G-y~T~YaHlS~~  565 (652)
                           .+-|.-|    |=.=.+==| |.++---+ |-+.-.=|+--|++||||+| ..+.---|+.-
T Consensus       451 rL~~Lik~HDvVFLl~DsRE~RWLPtvLc~~~~K-IaI~aAlGFDsY~v~RHG~gs~~~~~~d~~~~  516 (689)
T TIGR01381       451 RLEELIKEHDVVFLLLDSREARWLPTVLCARFDK-IAISAALGFDSYLVMRHGAGSRSEEVSDVEES  516 (689)
T ss_pred             HHHHHHHHCCEEEEECCCCHHHHHHHHHHHCCCC-EEEEEEECCCEEEEEECCCCCCCCCHHHHHHC
T ss_conf             9999865005355301365002237899753794-48887423360577762788865302335442


No 166
>PTZ00085 40S ribosomal protein S28; Provisional
Probab=31.26  E-value=15  Score=15.59  Aligned_cols=53  Identities=19%  Similarity=0.285  Sum_probs=27.2

Q ss_pred             CCEEEEECCCCCCCCCEEEEEEEECCEECCCCEECCCCCCCCCHHHHHHHHHHHH
Q ss_conf             9589984166788874268899786788366200078878788899999999999
Q gi|254780879|r  578 GQIIGWIGTTGLSTGPHLHYELIVNGIKVDSTKVRIPERENLKGDLLQRFAMEKK  632 (652)
Q Consensus       578 GQvIG~vGsTG~STGPHLHfEv~vnG~~VdP~~~~lp~~~~l~~~~l~~F~~~~~  632 (652)
                      =+|+|..||+|-.|.  +.-||+-++..-+-.-++.-.|..-.|+.|.=.+.||+
T Consensus        10 ~~vlGRTG~~G~~tQ--Vrv~~l~~~~~~gR~i~RNVkGPVr~GDIL~LlEtERE   62 (67)
T PTZ00085         10 EKVLGRTGSRGGVTQ--VRVQFMGESELEGRTLIRNVKGPVREGDILALLETERE   62 (67)
T ss_pred             EEEECCCCCCCCEEE--EEEEEECCCCCCCCEEEEECCCCCCCCCEEEEEHHHHH
T ss_conf             999525557686799--99999218886686988804277335649875214446


No 167
>PTZ00144 dihydrolipoamide succinyltransferase; Provisional
Probab=30.82  E-value=31  Score=13.49  Aligned_cols=23  Identities=9%  Similarity=0.059  Sum_probs=15.0

Q ss_pred             CCEECCCCCCCCCHHHHHHHHHHH
Q ss_conf             620007887878889999999999
Q gi|254780879|r  608 STKVRIPERENLKGDLLQRFAMEK  631 (652)
Q Consensus       608 P~~~~lp~~~~l~~~~l~~F~~~~  631 (652)
                      ++.+ --..|.++|..-++|....
T Consensus       395 ~lsL-s~DHRviDGa~aArFl~~l  417 (430)
T PTZ00144        395 NLAL-TYDHRLIDGRDAVQFLNAI  417 (430)
T ss_pred             EEEE-EEECCCCCHHHHHHHHHHH
T ss_conf             9889-7233030639999999999


No 168
>COG1912 Uncharacterized conserved protein [Function unknown]
Probab=30.42  E-value=31  Score=13.44  Aligned_cols=46  Identities=22%  Similarity=0.356  Sum_probs=32.8

Q ss_pred             EEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCCCEEEEEEEEC-CEECCCCEECC
Q ss_conf             200214454118899788349589984166788874268899786-78836620007
Q gi|254780879|r  558 SYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTGPHLHYELIVN-GIKVDSTKVRI  613 (652)
Q Consensus       558 ~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STGPHLHfEv~vn-G~~VdP~~~~l  613 (652)
                      .|.+.-+|   ++.=-.|..||.+.|+||       |-|.||-+| |..-+-+.++.
T Consensus       213 ~~~~k~~~---v~tfg~v~~Ge~l~~~nS-------~g~lEiaVn~Gsaa~~l~v~~  259 (268)
T COG1912         213 VYGNKIPF---VKTFGDVDEGELLALINS-------LGNLEIAVNMGSAAEKLGVKE  259 (268)
T ss_pred             EEEEEEEE---EEEECCCCCCCEEEEECC-------CCCEEEEEECCCHHHHHCCCC
T ss_conf             86217656---731134788976898658-------770899985488889719887


No 169
>COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=29.86  E-value=32  Score=13.38  Aligned_cols=14  Identities=7%  Similarity=0.147  Sum_probs=8.8

Q ss_pred             CCCCCEEEEEEEEE
Q ss_conf             14454068875321
Q gi|254780879|r  421 LKPTDFLETFFSVN  434 (652)
Q Consensus       421 ir~GD~f~Vlye~~  434 (652)
                      .+--|+.-|+|...
T Consensus       218 a~~aDrv~VMYaG~  231 (316)
T COG0444         218 AEIADRVAVMYAGR  231 (316)
T ss_pred             HHHCCEEEEEECCE
T ss_conf             97456689987758


No 170
>pfam08710 nsp9 nsp9 replicase. nsp9 is a single-stranded RNA-binding viral protein likely to be involved in RNA synthesis. Its structure comprises of a single beta barrel.
Probab=29.40  E-value=32  Score=13.33  Aligned_cols=33  Identities=24%  Similarity=0.417  Sum_probs=21.9

Q ss_pred             ECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCC
Q ss_conf             839974882002144541188997883495899841667
Q gi|254780879|r  550 HHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTG  588 (652)
Q Consensus       550 ~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG  588 (652)
                      +-++|-+-.|..-      ||--...++|.|+|+.|+|=
T Consensus        76 ~~~~g~~vkYLYF------VKnln~L~RG~VlG~I~aTV  108 (111)
T pfam08710        76 DTPKGPEVKYLYF------VKNLNNLRRGAVLGYIGATV  108 (111)
T ss_pred             ECCCCCEEEEEEE------ECCCCHHHCCEEEEEEEEEE
T ss_conf             8699978999998------61643010003887633799


No 171
>TIGR01348 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006256   This group of sequences are a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and percent identity (UPGMA) trees. Members contain two or three copies of the lipoyl-binding domain. Escherichia coli AceF is included in this set while mitochondrial and some other bacterial forms are excluded.  dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase complex; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006096 glycolysis, 0045254 pyruvate dehydrogenase complex.
Probab=29.25  E-value=31  Score=13.41  Aligned_cols=31  Identities=6%  Similarity=-0.021  Sum_probs=20.4

Q ss_pred             EEEEEECCEEEEEECCCEEEEECCCCCCCCCCCCCC
Q ss_conf             114766674247645710021002365533358979
Q gi|254780879|r  118 PTLIKDHNKDIIKKIPFAYARMTFATPYPKVKDHPK  153 (652)
Q Consensus       118 ~~~~~~g~r~~~~~~pf~~~~~~l~~~~~~~~~~p~  153 (652)
                      ++-.++||     +.+--++-|.|-.....++.-|.
T Consensus        56 ~ikvkVGD-----t~~~G~~i~~l~~~~g~a~aaPa   86 (655)
T TIGR01348        56 EIKVKVGD-----TLKEGDVIALLEVSAGSASAAPA   86 (655)
T ss_pred             EEEEEECC-----CCCCCCEEEEECCCCCCCCCCCC
T ss_conf             89754466-----54778789997166532135776


No 172
>TIGR01437 selA_rel pyridoxal phosphate-dependent enzyme, putative; InterPro: IPR006337    Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .   PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic .   This entry represents a group of proteins that are related to a number of pyridoxal phosphate-dependent enzymes, and in particular to selenocysteine synthase (SelA), which converts Ser to selenocysteine on its tRNA. While resembling SelA, this protein is found only in species that have a better candidate SelA or else lack the other genes (selB, selC, and selD) required for selenocysteine incorporation. .
Probab=29.13  E-value=16  Score=15.54  Aligned_cols=22  Identities=41%  Similarity=0.382  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHH-HHHHCCCCCCC
Q ss_conf             99999999999-87626884100
Q gi|254780879|r   51 ITSGVIIGGSL-LTALDGHQKIA   72 (652)
Q Consensus        51 ~~~~~l~g~a~-~~aldg~~~~a   72 (652)
                      ||+|+==|.|+ .|||=+....+
T Consensus        66 Its~AsAGia~~vAali~~g~~a   88 (391)
T TIGR01437        66 ITSGASAGIALAVAALISKGTRA   88 (391)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             89878889999999975167632


No 173
>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR).  DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes.  Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.
Probab=29.10  E-value=33  Score=13.29  Aligned_cols=47  Identities=11%  Similarity=-0.044  Sum_probs=19.5

Q ss_pred             CCCCCCCCCCCCCC-CCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             34222665445677-7764013688417970899999749998999999
Q gi|254780879|r  257 ENRTITSPQVLIDK-IPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKI  304 (652)
Q Consensus       257 en~t~~~~~~~~~~-~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i  304 (652)
                      +|++..-+...... .+--..-...|++|+.+ .|+-..|--.....++
T Consensus         7 ~nls~~y~~~~~~~~k~iL~~vs~~v~~Gei~-~ilGpnGaGKSTLl~~   54 (194)
T cd03213           7 RNLTVTVKSSPSKSGKQLLKNVSGKAKPGELT-AIMGPSGAGKSTLLNA   54 (194)
T ss_pred             EEEEEEECCCCCCCCCEEEECCEEEEECCEEE-EEECCCCCHHHHHHHH
T ss_conf             98999978999889998788838899088199-9998999519999999


No 174
>cd00421 intradiol_dioxygenase Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear non-heme iron enzymes that catalyze the oxygenation of catecholates to aliphatic acids via the cleavage of aromatic rings. The members are intradiol-cleaving enzymes which break the catechol C1-C2 bond and utilize Fe3+, as opposed to the extradiol-cleaving enzymes which break the C2-C3 or C1-C6 bond and utilize Fe2+ and Mn+. Catechol 1,2-dioxygenases are mostly homodimers with one catalytic ferric ion per monomer. Protocatechuate 3,4-dioxygenases form more diverse oligomers.
Probab=28.83  E-value=33  Score=13.26  Aligned_cols=13  Identities=31%  Similarity=0.897  Sum_probs=11.2

Q ss_pred             CCEEEEEEEECCE
Q ss_conf             7426889978678
Q gi|254780879|r  592 GPHLHYELIVNGI  604 (652)
Q Consensus       592 GPHLHfEv~vnG~  604 (652)
                      -||+||.|..+|.
T Consensus        83 ~~HIH~~v~~~g~   95 (146)
T cd00421          83 PPHIHFKVFAPGY   95 (146)
T ss_pred             CCEEEEEEECCCC
T ss_conf             8759999981996


No 175
>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=28.81  E-value=33  Score=13.26  Aligned_cols=11  Identities=36%  Similarity=0.610  Sum_probs=3.6

Q ss_pred             EEECCCCEEEE
Q ss_conf             79715967999
Q gi|254780879|r  526 IVAVGDGIVEK  536 (652)
Q Consensus       526 I~Aag~G~V~~  536 (652)
                      |+--.+|+|+.
T Consensus       206 Iivl~~G~ive  216 (234)
T cd03251         206 IVVLEDGKIVE  216 (234)
T ss_pred             EEEEECCEEEE
T ss_conf             99998999999


No 176
>KOG0215 consensus
Probab=28.74  E-value=33  Score=13.25  Aligned_cols=101  Identities=21%  Similarity=0.258  Sum_probs=57.7

Q ss_pred             EECCCCCEEEEECCCCEEEEEHHH--------------------------HHHHHCCCCCCEEECCCEEEEE---CCCCC
Q ss_conf             308970079998399748820021--------------------------4454118899788349589984---16678
Q gi|254780879|r  539 WAGGYGKQTLIHHGNGYVSSYNHQ--------------------------DAIAKNIKAGTAVKQGQIIGWI---GTTGL  589 (652)
Q Consensus       539 ~~~GyGn~V~I~H~~Gy~T~YaHl--------------------------S~~a~gV~~G~~V~qGQvIG~v---GsTG~  589 (652)
                      -+.|||++.+-+|.-...-.|++.                          +.+   +.+|.+|+-||++=--   -.||.
T Consensus       783 lDRGfGRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~kh~vLd~DGl---~~pG~~V~~~qi~iNK~mP~vt~~  859 (1153)
T KOG0215         783 IDRGFGRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIWKHQVLDDDGL---ATPGERVQPGQIYINKQMPTVTGT  859 (1153)
T ss_pred             HCCCCCEEEEEEEEEEEEEECCCCCHHHHCCCCCCCCCCCCCHHHCCCCCCCC---CCCCCEECCCCEEEECCCCCCCCC
T ss_conf             11575248998600666640578751332365447876783022115375557---787537326857982567875566


Q ss_pred             CCCCEEEEEEEECCEECCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             88742688997867883662000788787888999999999999999984147766
Q gi|254780879|r  590 STGPHLHYELIVNGIKVDSTKVRIPERENLKGDLLQRFAMEKKRINSLLNNGENPK  645 (652)
Q Consensus       590 STGPHLHfEv~vnG~~VdP~~~~lp~~~~l~~~~l~~F~~~~~~id~ll~~~~~~~  645 (652)
                       ..|-+|--  .++-.--|+..|-|...-++.-++..=..+---|.-||..-++|+
T Consensus       860 -~~~~~~~~--~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQTRrPE  912 (1153)
T KOG0215         860 -SLPGLSAS--QVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPE  912 (1153)
T ss_pred             -CCCCCCCC--CCCCCCCCCEECCCCCCHHHEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             -57777765--533321641433898232122676227432189999986436864


No 177
>KOG1885 consensus
Probab=28.63  E-value=33  Score=13.24  Aligned_cols=34  Identities=24%  Similarity=0.410  Sum_probs=19.0

Q ss_pred             EEEEEEECCEEC-CCCEECCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             688997867883-662000788787888999999999999
Q gi|254780879|r  595 LHYELIVNGIKV-DSTKVRIPERENLKGDLLQRFAMEKKR  633 (652)
Q Consensus       595 LHfEv~vnG~~V-dP~~~~lp~~~~l~~~~l~~F~~~~~~  633 (652)
                      =.||+.++|+-+ |-.+ .|    .=+-.+++.|+.|...
T Consensus       465 eRFElFi~~kEicNAYt-El----NdP~~Qr~rFe~Q~~~  499 (560)
T KOG1885         465 ERFELFIAGKEICNAYT-EL----NDPVDQRQRFEQQARD  499 (560)
T ss_pred             HHHHHHHCCHHHHHHHH-HH----CCHHHHHHHHHHHHHH
T ss_conf             67787541088754666-60----6889999999999877


No 178
>TIGR02408 ectoine_ThpD ectoine hydroxylase; InterPro: IPR012774    Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.; GO: 0016725 oxidoreductase activity acting on CH or CH2 groups.
Probab=28.44  E-value=17  Score=15.25  Aligned_cols=10  Identities=10%  Similarity=0.159  Sum_probs=5.1

Q ss_pred             HHHCCCCHHH
Q ss_conf             8871999899
Q gi|254780879|r  394 TSFNGMNSNL  403 (652)
Q Consensus       394 a~~~gip~~i  403 (652)
                      ++..|+|...
T Consensus       190 ~Q~~GvPd~~  199 (278)
T TIGR02408       190 KQEVGVPDEV  199 (278)
T ss_pred             CCCCCCCCHH
T ss_conf             0678898778


No 179
>cd03288 ABCC_SUR2 The SUR domain 2.  The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family.  Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel.  Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism.  It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
Probab=28.01  E-value=34  Score=13.17  Aligned_cols=44  Identities=9%  Similarity=-0.001  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHH
Q ss_conf             334222665445677776401368841797089999974999899999
Q gi|254780879|r  256 EENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAK  303 (652)
Q Consensus       256 ~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~  303 (652)
                      =+|+++.-+....   +....-...|++|+.+. |.-+.|--...+.+
T Consensus        22 ~~nvsf~Y~~~~~---~vL~~inl~I~~Ge~va-IvG~sGsGKSTL~~   65 (257)
T cd03288          22 IHDLCVRYENNLK---PVLKHVKAYIKPGQKVG-ICGRTGSGKSSLSL   65 (257)
T ss_pred             EEEEEEEECCCCC---CCEECEEEEECCCCEEE-EECCCCCCHHHHHH
T ss_conf             9989999398995---73105389987999999-99999981999999


No 180
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop.  Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS).  aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA.  In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=27.97  E-value=34  Score=13.16  Aligned_cols=70  Identities=17%  Similarity=0.271  Sum_probs=39.3

Q ss_pred             EEEEEEE---CCCCC--EEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECCCCCCCC---CEEEEEEEECC
Q ss_conf             9996530---89700--79998399748820021445411889978834958998416678887---42688997867
Q gi|254780879|r  534 VEKANWA---GGYGK--QTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGTTGLSTG---PHLHYELIVNG  603 (652)
Q Consensus       534 V~~ag~~---~GyGn--~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGsTG~STG---PHLHfEv~vnG  603 (652)
                      |.-+||-   ...|+  ++.||.+.|..-.+.+.+......+.=...+.|.+|.-.|.--.+..   +.-.|||.+..
T Consensus         2 V~v~Gwv~~~R~~g~~~Fi~lrD~~g~iQvv~~~~~~~~~~~~~~~l~~es~I~v~G~v~~~~~~~~~~g~~Ei~~~~   79 (85)
T cd04100           2 VTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEE   79 (85)
T ss_pred             EEEEEEEEEEECCCCEEEEEEECCCCEEEEEECCCCCHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCCCEEEEEEE
T ss_conf             999998790432898899585038950899991775857887763589888999999999688777899889999939


No 181
>PRK00624 glycine cleavage system protein H; Provisional
Probab=27.94  E-value=34  Score=13.16  Aligned_cols=19  Identities=16%  Similarity=0.421  Sum_probs=8.1

Q ss_pred             CCCCEEECCCEEEEECCCC
Q ss_conf             8997883495899841667
Q gi|254780879|r  570 KAGTAVKQGQIIGWIGTTG  588 (652)
Q Consensus       570 ~~G~~V~qGQvIG~vGsTG  588 (652)
                      +.|++|++|+.+|.+-|..
T Consensus        40 ~~G~~v~~g~~~~~iEs~K   58 (113)
T PRK00624         40 SVGSFCKEGEVLVILESSK   58 (113)
T ss_pred             CCCCEEECCCEEEEEEECC
T ss_conf             9999884798599999652


No 182
>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=27.57  E-value=35  Score=13.11  Aligned_cols=16  Identities=13%  Similarity=0.302  Sum_probs=10.3

Q ss_pred             CCEEECCCCEEEEEEE
Q ss_conf             7279715967999653
Q gi|254780879|r  524 TPIVAVGDGIVEKANW  539 (652)
Q Consensus       524 TPI~Aag~G~V~~ag~  539 (652)
                      .-|+=-.+|.|+..|.
T Consensus       517 D~I~vl~~G~ive~Gt  532 (569)
T PRK10789        517 SEIIVMQHGHIAQRGN  532 (569)
T ss_pred             CEEEEEECCEEEEECC
T ss_conf             9899998988999727


No 183
>PRK12999 pyruvate carboxylase; Reviewed
Probab=27.45  E-value=35  Score=13.10  Aligned_cols=16  Identities=38%  Similarity=0.501  Sum_probs=9.2

Q ss_pred             CCCCCEEECCCEEEEE
Q ss_conf             8899788349589984
Q gi|254780879|r  569 IKAGTAVKQGQIIGWI  584 (652)
Q Consensus       569 V~~G~~V~qGQvIG~v  584 (652)
                      |++|++|++||.+--+
T Consensus      1093 Vk~GD~VkkGd~Llvl 1108 (1147)
T PRK12999       1093 VKEGDEVKAGDPLLVI 1108 (1147)
T ss_pred             ECCCCEECCCCEEEEE
T ss_conf             6899987899989998


No 184
>PRK09473 oppD oligopeptide transporter ATP-binding component; Provisional
Probab=27.41  E-value=35  Score=13.09  Aligned_cols=24  Identities=8%  Similarity=0.300  Sum_probs=12.6

Q ss_pred             ECCCCCHHHHHHH-CCCCHHHHHHH
Q ss_conf             4179708999997-49998999999
Q gi|254780879|r  281 IQHNTTIFDAMVH-AGYSNGDSAKI  304 (652)
Q Consensus       281 VK~GDTL~~IL~r-~Gvs~~ei~~i  304 (652)
                      .+-|+.+...+.. .+++..++.+-
T Consensus       114 ~~i~~~l~e~l~~~~~~~~~~~~~~  138 (330)
T PRK09473        114 MRVGEQLMEVLMLHKGMSKAEAFEE  138 (330)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             0456655578988538998999999


No 185
>PTZ00109 DNA gyrase subunit b; Provisional
Probab=27.39  E-value=35  Score=13.09  Aligned_cols=19  Identities=16%  Similarity=0.263  Sum_probs=13.7

Q ss_pred             CCCHHHHHHHHHHHCCCCH
Q ss_conf             9998999999997301110
Q gi|254780879|r  398 GMNSNLVKLIMRTLASSVN  416 (652)
Q Consensus       398 gip~~ii~~lv~i~a~dVD  416 (652)
                      -+...-|..|+..++..|.
T Consensus       624 il~N~EI~~LItAlG~Gig  642 (941)
T PTZ00109        624 IFENSELKSLITAIGLNVN  642 (941)
T ss_pred             HHCCHHHHHHHHHHCCCCC
T ss_conf             4404999999998586867


No 186
>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain.  They export degradative enzymes by using a type I protein secretion system and  lack an N-terminal signal peptide, but contain a C-terminal secretion signal.  The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP).  For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli.  The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior.  HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels.  The spectrum of transport substra
Probab=27.02  E-value=35  Score=13.05  Aligned_cols=30  Identities=10%  Similarity=0.195  Sum_probs=14.8

Q ss_pred             CCEEEEEECCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             4013688417970899999749998999999
Q gi|254780879|r  274 FADDLIPIQHNTTIFDAMVHAGYSNGDSAKI  304 (652)
Q Consensus       274 ~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i  304 (652)
                      ...-...|++|+.+. |.-..|--.....++
T Consensus        18 L~~i~l~i~~G~~va-IvG~sGsGKSTLl~l   47 (173)
T cd03246          18 LRNVSFSIEPGESLA-IIGPSGSGKSTLARL   47 (173)
T ss_pred             EECEEEEECCCCEEE-EECCCCCHHHHHHHH
T ss_conf             547699985999999-999999809999999


No 187
>PRK11022 dppD dipeptide transporter ATP-binding subunit; Provisional
Probab=26.70  E-value=36  Score=13.01  Aligned_cols=13  Identities=0%  Similarity=0.118  Sum_probs=8.8

Q ss_pred             CCCCEEEEEEEEE
Q ss_conf             4454068875321
Q gi|254780879|r  422 KPTDFLETFFSVN  434 (652)
Q Consensus       422 r~GD~f~Vlye~~  434 (652)
                      +-.|++-|+|...
T Consensus       219 ~~aDri~VMy~G~  231 (327)
T PRK11022        219 EAAHKIIVMYAGQ  231 (327)
T ss_pred             HHCCEEEEEECCE
T ss_conf             8699899998988


No 188
>pfam04203 Sortase Sortase family. The founder member of this family is S.aureus sortase, a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall.
Probab=26.62  E-value=36  Score=13.00  Aligned_cols=28  Identities=21%  Similarity=0.389  Sum_probs=12.2

Q ss_pred             CCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEE
Q ss_conf             700799983997488200214454118899788
Q gi|254780879|r  543 YGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAV  575 (652)
Q Consensus       543 yGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V  575 (652)
                      -||.|+-=|. ++-+.+++|..    +++|+.|
T Consensus        38 ~gn~viaGH~-~~~~~F~~L~~----l~~Gd~i   65 (122)
T pfam04203        38 GGNTVIAGHR-GGGTMFSRLDK----LKKGDKI   65 (122)
T ss_pred             CCCEEEEEEE-CCCCHHHHHHC----CCCCCEE
T ss_conf             8729999873-89921335652----8899999


No 189
>pfam04017 DUF366 Domain of unknown function (DUF366). Archaeal domain of unknown function.
Probab=26.50  E-value=24  Score=14.27  Aligned_cols=13  Identities=15%  Similarity=0.120  Sum_probs=5.7

Q ss_pred             CHHHCCCCCEEEE
Q ss_conf             6101699888999
Q gi|254780879|r  313 RVDQLTKDEILRI  325 (652)
Q Consensus       313 ~~~~Lr~Gq~L~I  325 (652)
                      ...-.+.|+-|-+
T Consensus        99 g~~~~r~GDDlyv  111 (183)
T pfam04017        99 GVKLTRDGDDLYV  111 (183)
T ss_pred             CCCCEECCCEEEE
T ss_conf             9860655781687


No 190
>TIGR00030 S21p ribosomal protein S21; InterPro: IPR001911   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryote ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA . The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome , and is one of the 'split proteins': these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=26.28  E-value=36  Score=12.96  Aligned_cols=18  Identities=11%  Similarity=0.157  Sum_probs=15.5

Q ss_pred             EEEECCCCCHHHHHHHCC
Q ss_conf             688417970899999749
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAG  295 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~G  295 (652)
                      .|.|+.||+|..+|++..
T Consensus         2 ~V~V~eges~d~ALr~FK   19 (58)
T TIGR00030         2 TVKVKEGESIDSALRRFK   19 (58)
T ss_pred             EEEECCCCCHHHHHHHHH
T ss_conf             025115887889999985


No 191
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases.  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=26.13  E-value=37  Score=12.94  Aligned_cols=12  Identities=17%  Similarity=0.039  Sum_probs=5.7

Q ss_pred             HHHCCCCHHHHH
Q ss_conf             997499989999
Q gi|254780879|r  291 MVHAGYSNGDSA  302 (652)
Q Consensus       291 L~r~Gvs~~ei~  302 (652)
                      .+..|++..++.
T Consensus        46 Ar~lgv~~~~ig   57 (319)
T cd02577          46 AKALGISRKRIG   57 (319)
T ss_pred             HHHHCCCHHHEE
T ss_conf             998299877751


No 192
>COG1038 PycA Pyruvate carboxylase [Energy production and conversion]
Probab=26.11  E-value=31  Score=13.50  Aligned_cols=23  Identities=30%  Similarity=0.567  Sum_probs=15.3

Q ss_pred             CCCCCEEECCCEEEEECCCCCCC
Q ss_conf             88997883495899841667888
Q gi|254780879|r  569 IKAGTAVKQGQIIGWIGTTGLST  591 (652)
Q Consensus       569 V~~G~~V~qGQvIG~vGsTG~ST  591 (652)
                      |++|++|++||++.-.-.--.-|
T Consensus      1095 V~~G~~Vk~Gd~l~~ieAMKMEt 1117 (1149)
T COG1038        1095 VKKGDKVKKGDVLAVIEAMKMET 1117 (1149)
T ss_pred             ECCCCCCCCCCEEEEEHHHHHCE
T ss_conf             74587304798653302232222


No 193
>PRK07440 hypothetical protein; Provisional
Probab=26.06  E-value=16  Score=15.47  Aligned_cols=48  Identities=17%  Similarity=0.067  Sum_probs=30.6

Q ss_pred             EEECCCCCHHHHHHHCCCCHHHHHHHHH---HHHCCCCHHHCCCCCEEEEE
Q ss_conf             8841797089999974999899999999---85401561016998889999
Q gi|254780879|r  279 IPIQHNTTIFDAMVHAGYSNGDSAKIAK---ALKNEVRVDQLTKDEILRIG  326 (652)
Q Consensus       279 v~VK~GDTL~~IL~r~Gvs~~ei~~i~~---al~~~~~~~~Lr~Gq~L~I~  326 (652)
                      ..+..+-||.++|...++.+.-++-..+   ..+..++...|+.|+++.|.
T Consensus        14 ~~~~~~~ti~~LL~~l~~~~~~vaVE~N~~Iv~r~~~~~~~l~~gD~iEIv   64 (70)
T PRK07440         14 RTCSPGTTLPDLLQQLGFNPRLVAVEYNGEILHRQFWEQTQVQPGDRLEIV   64 (70)
T ss_pred             EECCCCCCHHHHHHHCCCCCCEEEEEECCEEECHHHCCCEECCCCCEEEEE
T ss_conf             785999989999987699987699996886708677071067999999999


No 194
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis.  The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes.  CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space.  In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=26.00  E-value=37  Score=12.92  Aligned_cols=29  Identities=7%  Similarity=0.150  Sum_probs=12.9

Q ss_pred             CEEEEEECCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             013688417970899999749998999999
Q gi|254780879|r  275 ADDLIPIQHNTTIFDAMVHAGYSNGDSAKI  304 (652)
Q Consensus       275 ~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i  304 (652)
                      ..-...|++|+.+. |+-..|--.....++
T Consensus        19 ~~i~l~i~~Ge~~a-ivG~sGsGKSTLl~~   47 (178)
T cd03247          19 KNLSLELKQGEKIA-LLGRSGSGKSTLLQL   47 (178)
T ss_pred             ECEEEEECCCCEEE-EECCCCCHHHHHHHH
T ss_conf             25589986999999-999998759999999


No 195
>cd00257 Fascin Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed;  identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast  growth factor (FGF)
Probab=25.99  E-value=37  Score=12.92  Aligned_cols=51  Identities=20%  Similarity=0.160  Sum_probs=30.3

Q ss_pred             EEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHH
Q ss_conf             030267967279715967999653089700799983997488200214454
Q gi|254780879|r  516 VDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIA  566 (652)
Q Consensus       516 VD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a  566 (652)
                      +-+.+.-|--+.+..+|.|.-.+-.+.-..+.++.|++|-.+.-++.-+|.
T Consensus        46 ~~lrs~~Gkyl~~~~~g~i~~~~~~~~~~~F~~e~~~~g~valka~nG~Yl   96 (119)
T cd00257          46 YALRSHDGKYLSADSDGGVQLEGHPNADCRFTLEFHGDGKWALRAENGRYL   96 (119)
T ss_pred             EEEEECCCCEEEECCCCCEEEECCCCCCCEEEEEEECCCEEEEECCCCCEE
T ss_conf             999956899999858998886057899976999991798699984899899


No 196
>pfam06898 YqfD Putative stage IV sporulation protein YqfD. This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis is known to be essential for efficient sporulation although its exact function is unknown.
Probab=25.80  E-value=37  Score=12.90  Aligned_cols=10  Identities=20%  Similarity=0.514  Sum_probs=3.3

Q ss_pred             EEEEEEECCC
Q ss_conf             3688962388
Q gi|254780879|r  446 LLYIHARFGE  455 (652)
Q Consensus       446 il~A~~~~~g  455 (652)
                      +.++.....|
T Consensus       158 i~Wv~v~i~G  167 (383)
T pfam06898       158 IMWIGVRVRG  167 (383)
T ss_pred             EEEEEEEEEE
T ss_conf             2999999983


No 197
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=25.73  E-value=37  Score=12.89  Aligned_cols=21  Identities=19%  Similarity=0.289  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9989899999999999999987
Q gi|254780879|r   42 WLSTTFFAGITSGVIIGGSLLT   63 (652)
Q Consensus        42 w~~~t~ltg~~~~~l~g~a~~~   63 (652)
                      ++.-++++.+++. +.|.-+|.
T Consensus        16 ~~~~~~~~~~~a~-~~~~~~~~   36 (352)
T COG1566          16 KLPLTLLVVLAAV-LYGGLIWL   36 (352)
T ss_pred             HHHHHHHHHHHHH-HHHHHHHH
T ss_conf             8899999999999-99999999


No 198
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=25.48  E-value=33  Score=13.24  Aligned_cols=30  Identities=10%  Similarity=0.148  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHCCCCHHHCCCCCEEEEEE
Q ss_conf             899999999854015610169988899997
Q gi|254780879|r  298 NGDSAKIAKALKNEVRVDQLTKDEILRIGV  327 (652)
Q Consensus       298 ~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~  327 (652)
                      .+.|.++..++..+.....=...+.+.+++
T Consensus       186 ~~~i~eLm~avd~yip~Per~~dkPflmpv  215 (394)
T COG0050         186 EAKIEELMDAVDSYIPTPERDIDKPFLMPV  215 (394)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             789999999998548999865566520101


No 199
>pfam07126 DUF1379 Protein of unknown function (DUF1379). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.
Probab=25.47  E-value=38  Score=12.86  Aligned_cols=51  Identities=12%  Similarity=0.139  Sum_probs=23.1

Q ss_pred             CEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEE
Q ss_conf             67999653089700799983997488200214454118899788349589984
Q gi|254780879|r  532 GIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWI  584 (652)
Q Consensus       532 G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~v  584 (652)
                      |.|+.-.-.+..|.+++|+++..-.+--.=-..+.  +..-..-+|||+|=-+
T Consensus        90 g~~v~L~~~~~~~~flVvE~g~~asLCll~~~~~~--L~~~K~l~~~~~IKVM  140 (154)
T pfam07126        90 GDLVQLKSGGETGLFLVVENGEQASLCLLLSEEFQ--LSGSKTLVQFDVIKVM  140 (154)
T ss_pred             CCEEEECCCCCEEEEEEEECCCCEEEEEECCCCEE--ECCCCEEECCCEEEEE
T ss_conf             88899813895689999946996778887356424--0887416268738998


No 200
>COG5526 Lysozyme family protein [General function prediction only]
Probab=25.42  E-value=33  Score=13.26  Aligned_cols=21  Identities=33%  Similarity=0.330  Sum_probs=9.9

Q ss_pred             HHHCCCCHHHHHCCCCCEEEE
Q ss_conf             973011101210144540688
Q gi|254780879|r  409 RTLASSVNLQEHLKPTDFLET  429 (652)
Q Consensus       409 ~i~a~dVDFqr~ir~GD~f~V  429 (652)
                      .......||..-+..||.+..
T Consensus        65 H~~E~SlnF~thLhNGdpL~a   85 (191)
T COG5526          65 HYRESSLNFGTHLHNGDPLGA   85 (191)
T ss_pred             HHHHCCCCCCCCCCCCCCCCC
T ss_conf             431123543432468984566


No 201
>PRK05644 gyrB DNA gyrase subunit B; Validated
Probab=25.34  E-value=38  Score=12.84  Aligned_cols=16  Identities=13%  Similarity=0.358  Sum_probs=6.9

Q ss_pred             CHHHHHHHHHHHCCCC
Q ss_conf             9899999999730111
Q gi|254780879|r  400 NSNLVKLIMRTLASSV  415 (652)
Q Consensus       400 p~~ii~~lv~i~a~dV  415 (652)
                      ...-|..|+.+++.++
T Consensus       469 ~N~EI~~li~alG~g~  484 (725)
T PRK05644        469 SSEEIGTLITALGTGI  484 (725)
T ss_pred             CCHHHHHHHHHHCCCC
T ss_conf             1879999999967788


No 202
>TIGR00955 3a01204 Pigment precourser permease; InterPro: IPR005284   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This family includes different parts of a membrane-spanning permease system necessary for the transport of pigment precursor into pigment cells responsible for eye color. White protein dimerises with brown protein for the transport of guanine and with scarlet protein for the transport of tryptophan.; GO: 0006810 transport.
Probab=25.31  E-value=38  Score=12.84  Aligned_cols=58  Identities=12%  Similarity=0.135  Sum_probs=35.0

Q ss_pred             CCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCC-----EEE----EEEECCCCCEEEEEEECCCC
Q ss_conf             9998999999998540156101699888999972788864-----058----99971688348999842788
Q gi|254780879|r  295 GYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQKDDKF-----TIV----RFSIYHKQKHLLTIALNDNN  357 (652)
Q Consensus       295 Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~~~~~~-----~~~----r~si~~~~~~~~~va~~d~g  357 (652)
                      |+|.-.+..+++.|+++.     +.|..+.+.+.++....     ++.    --.+|.++..++.-=.++-|
T Consensus       205 GLDSfmA~~Vv~~L~~LA-----~~G~tiI~tIHQPSs~lF~lFd~i~lla~Grvvy~G~p~~a~~FF~~~G  271 (671)
T TIGR00955       205 GLDSFMAYSVVQVLKGLA-----QKGKTIICTIHQPSSELFELFDKIILLAEGRVVYLGSPDQAVPFFSELG  271 (671)
T ss_pred             HHHHHHHHHHHHHHHHHH-----CCCCEEEEEEECCCHHHHHHHCCEEEEECCEEEEECCCHHHHHHHHHCC
T ss_conf             345999999999999985-----0897999983056188985117167752772798278103689898448


No 203
>cd03812 GT1_CapH_like This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1).
Probab=25.29  E-value=38  Score=12.84  Aligned_cols=39  Identities=15%  Similarity=0.085  Sum_probs=25.0

Q ss_pred             ECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHH
Q ss_conf             02679672797159679996530897007999839974882002144541
Q gi|254780879|r  518 WAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAK  567 (652)
Q Consensus       518 ~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~  567 (652)
                      =|...|+||+|+..|           |+-++|..+.||.....--..+|.
T Consensus       285 EAma~G~PVVasd~g-----------g~~~ii~~~~~~l~~~~~~~~~a~  323 (358)
T cd03812         285 EAQASGLPCILSDTI-----------TKEVDLTDLVKFLSLDESPEIWAE  323 (358)
T ss_pred             HHHHHCCCEEEECCC-----------CCCEEEECCCCEEECCCCHHHHHH
T ss_conf             999949989996599-----------974697299557968999999999


No 204
>PRK12835 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=25.22  E-value=38  Score=12.83  Aligned_cols=25  Identities=4%  Similarity=-0.059  Sum_probs=17.0

Q ss_pred             CHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             1025666887199989999999973
Q gi|254780879|r  387 YDGIWRATSFNGMNSNLVKLIMRTL  411 (652)
Q Consensus       387 ~~SLy~aa~~~gip~~ii~~lv~i~  411 (652)
                      .+||-+.|.+.|++.....+-+.-|
T Consensus       429 adTleELA~~~gvd~~~L~~TV~rY  453 (584)
T PRK12835        429 AHTWDELAAKIGVPAENLRATAERF  453 (584)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             3999999988298989999999999


No 205
>PRK11176 lipid transporter ATP-binding/permease protein; Provisional
Probab=25.22  E-value=30  Score=13.57  Aligned_cols=46  Identities=20%  Similarity=0.169  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             23342226654456777764013688417970899999749998999999
Q gi|254780879|r  255 IEENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKI  304 (652)
Q Consensus       255 ~~en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i  304 (652)
                      .=+||++.-+....   +....-...+++|++++- .-+.|-....+.++
T Consensus       342 ~~~nVsF~Y~~~~~---~vL~~isl~I~~G~~vai-VG~SGsGKSTL~~L  387 (581)
T PRK11176        342 EFRNVTFTYPGKEV---PALRNINFKIPAGKTVAL-VGRSGSGKSTIANL  387 (581)
T ss_pred             EEEEEEEECCCCCC---CCCCCCCCCCCCCCEEEC-CCCCCCCHHHHHHH
T ss_conf             99985784489986---201066335799944312-28999867899999


No 206
>PRK07843 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=25.15  E-value=38  Score=12.82  Aligned_cols=34  Identities=6%  Similarity=0.121  Sum_probs=21.1

Q ss_pred             CCHHHHHHHHHCCCCHHHHHHHHHHH------CCCCHHHH
Q ss_conf             11025666887199989999999973------01110121
Q gi|254780879|r  386 IYDGIWRATSFNGMNSNLVKLIMRTL------ASSVNLQE  419 (652)
Q Consensus       386 I~~SLy~aa~~~gip~~ii~~lv~i~------a~dVDFqr  419 (652)
                      -.+||-+.|.+.|+|.....+-+.-|      +.|-||.|
T Consensus       418 kAdTleeLA~~~gi~~~~L~~Tv~~yN~~~~~G~D~dFgr  457 (560)
T PRK07843        418 KADTLAELAGKIGLPADALTATVQRFNGFARSGVDEDFHR  457 (560)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             4488999999969499999999999998885299855577


No 207
>PRK03481 consensus
Probab=25.01  E-value=38  Score=12.80  Aligned_cols=36  Identities=14%  Similarity=0.203  Sum_probs=23.1

Q ss_pred             CCCEEEEEHHH-HHHHHCCCCCCEEECCCEEEEECCC
Q ss_conf             99748820021-4454118899788349589984166
Q gi|254780879|r  552 GNGYVSSYNHQ-DAIAKNIKAGTAVKQGQIIGWIGTT  587 (652)
Q Consensus       552 ~~Gy~T~YaHl-S~~a~gV~~G~~V~qGQvIG~vGsT  587 (652)
                      |......+.-- =.+...+++|++|+-||-+|..-.|
T Consensus       253 GSTVIlLF~~~~~~~~~~l~~g~~vrmGe~la~~~~~  289 (322)
T PRK03481        253 GSTVINLFAPGKVNLAEQLNSLSVTRIGQPLAESTET  289 (322)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCCEEECCHHHHHCCCC
T ss_conf             8889999458853546345899746647665411212


No 208
>PRK05704 dihydrolipoamide succinyltransferase; Validated
Probab=24.99  E-value=38  Score=12.80  Aligned_cols=23  Identities=9%  Similarity=0.050  Sum_probs=15.6

Q ss_pred             CCEECCCCCCCCCHHHHHHHHHHH
Q ss_conf             620007887878889999999999
Q gi|254780879|r  608 STKVRIPERENLKGDLLQRFAMEK  631 (652)
Q Consensus       608 P~~~~lp~~~~l~~~~l~~F~~~~  631 (652)
                      ++.. --..|.++|..-++|....
T Consensus       370 ~lsl-s~DHRvidGa~aa~Fl~~l  392 (406)
T PRK05704        370 YLAL-SYDHRIIDGKEAVGFLVTI  392 (406)
T ss_pred             EEEE-EEECHHCCCHHHHHHHHHH
T ss_conf             9879-7452030739999999999


No 209
>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1).  NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters.  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.
Probab=24.91  E-value=39  Score=12.79  Aligned_cols=44  Identities=14%  Similarity=0.101  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             342226654456777764013688417970899999749998999999
Q gi|254780879|r  257 ENRTITSPQVLIDKIPEFADDLIPIQHNTTIFDAMVHAGYSNGDSAKI  304 (652)
Q Consensus       257 en~t~~~~~~~~~~~~~~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~i  304 (652)
                      +|+++.-....   .+....-...|++|+.+. |.-..|--...+.++
T Consensus        10 ~nvsf~Y~~~~---~~iL~~isl~i~~Ge~v~-ivG~sGsGKSTLl~l   53 (207)
T cd03369          10 ENLSVRYAPDL---PPVLKNVSFKVKAGEKIG-IVGRTGAGKSTLILA   53 (207)
T ss_pred             EEEEEECCCCC---CCCEEEEEEEECCCCEEE-EECCCCCCHHHHHHH
T ss_conf             98899929899---672402588986999999-999999879999999


No 210
>PRK04350 thymidine phosphorylase; Provisional
Probab=24.73  E-value=39  Score=12.76  Aligned_cols=53  Identities=26%  Similarity=0.270  Sum_probs=36.1

Q ss_pred             CCCCCCEEECCCCEEEEEEE--------ECCCCCEEEEECCCCEEEEEHHHHHHHHCCCCCCEEECCCEEEEECC
Q ss_conf             67967279715967999653--------08970079998399748820021445411889978834958998416
Q gi|254780879|r  520 APRGTPIVAVGDGIVEKANW--------AGGYGKQTLIHHGNGYVSSYNHQDAIAKNIKAGTAVKQGQIIGWIGT  586 (652)
Q Consensus       520 Ap~GTPI~Aag~G~V~~ag~--------~~GyGn~V~I~H~~Gy~T~YaHlS~~a~gV~~G~~V~qGQvIG~vGs  586 (652)
                      ++.=.+|.|..+|.|....-        .-|.|+    +|+-|..          -.+|.|++|++||.+..+=+
T Consensus       414 a~~~~~v~A~~~G~V~~ID~~~ig~~a~~aGAp~----D~~aGI~----------l~~KvGd~V~kGdpL~tIhA  474 (502)
T PRK04350        414 GDHTYDVLAPRDGYVTAIDNRRLARIARLAGAPK----DKGAGID----------LHKKIGDKVKKGDPLYTIYA  474 (502)
T ss_pred             CCEEEEEECCCCEEEEEECHHHHHHHHHHCCCCC----CCCCCEE----------EEECCCCEECCCCEEEEEEC
T ss_conf             8857999769984999851499999999719998----8704479----------96048799679984999966


No 211
>cd04949 GT1_gtfA_like This family is most closely related to the GT1 family of glycosyltransferases and is named after gtfA in Streptococcus gordonii, where it plays a role in the O-linked glycosylation of GspB, a cell surface glycoprotein involved in platelet binding.  In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltra
Probab=24.61  E-value=23  Score=14.35  Aligned_cols=42  Identities=31%  Similarity=0.582  Sum_probs=29.3

Q ss_pred             ECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECC-CCEEEEEHHHHHHHHCC
Q ss_conf             02679672797159679996530897007999839-97488200214454118
Q gi|254780879|r  518 WAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHG-NGYVSSYNHQDAIAKNI  569 (652)
Q Consensus       518 ~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~-~Gy~T~YaHlS~~a~gV  569 (652)
                      =|...|+||+|.          +-.||..-.|+|+ |||..-++--..++..|
T Consensus       297 EAma~GlPvIa~----------d~~yG~~eiI~~g~nG~Lv~~~d~~~la~~i  339 (372)
T cd04949         297 EALSHGLPVISY----------DVNYGPSEIIEDGENGYLVPKGDIEALAEAI  339 (372)
T ss_pred             HHHHCCCCEEEE----------CCCCCCHHHHCCCCCEEEECCCCHHHHHHHH
T ss_conf             999859999980----------5999968884589847996899999999999


No 212
>PRK10419 nikE nickel transporter ATP-binding protein; Provisional
Probab=24.57  E-value=39  Score=12.74  Aligned_cols=10  Identities=0%  Similarity=-0.273  Sum_probs=6.4

Q ss_pred             CCEEEEEEEE
Q ss_conf             5406887532
Q gi|254780879|r  424 TDFLETFFSV  433 (652)
Q Consensus       424 GD~f~Vlye~  433 (652)
                      .|++-|+|..
T Consensus       219 adri~Vm~~G  228 (266)
T PRK10419        219 CQRVMVMDNG  228 (266)
T ss_pred             CCEEEEEECC
T ss_conf             8989999898


No 213
>cd00728 malate_synt_G Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle.
Probab=24.40  E-value=9.8  Score=16.99  Aligned_cols=23  Identities=30%  Similarity=0.505  Sum_probs=10.0

Q ss_pred             EECCCEEEEECCCCCCCCCEEEE
Q ss_conf             83495899841667888742688
Q gi|254780879|r  575 VKQGQIIGWIGTTGLSTGPHLHY  597 (652)
Q Consensus       575 V~qGQvIG~vGsTG~STGPHLHf  597 (652)
                      -+.|---++|=|---+|=--|||
T Consensus       523 p~aGAn~AWVPSPTaAtLHA~HY  545 (712)
T cd00728         523 PKAGANTAWVPSPTAATLHALHY  545 (712)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             87876041578927898999888


No 214
>KOG3679 consensus
Probab=24.31  E-value=8.7  Score=17.32  Aligned_cols=45  Identities=29%  Similarity=0.486  Sum_probs=28.3

Q ss_pred             EEEEEEECCEECCCCE-ECCCCCCCCCHHHHHHHHHH----HHHHHHHHH
Q ss_conf             6889978678836620-00788787888999999999----999999984
Q gi|254780879|r  595 LHYELIVNGIKVDSTK-VRIPERENLKGDLLQRFAME----KKRINSLLN  639 (652)
Q Consensus       595 LHfEv~vnG~~VdP~~-~~lp~~~~l~~~~l~~F~~~----~~~id~ll~  639 (652)
                      -|||+++||....-+- -|.-.=|.+....|+.|+..    -+.+|.||+
T Consensus       566 hhfelringekleellseravqfraiqrrllarfkdktpaplqhldtlld  615 (802)
T KOG3679         566 HHFELRINGEKLEELLSERAVQFRAIQRRLLARFKDKTPAPLQHLDTLLD  615 (802)
T ss_pred             HEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHC
T ss_conf             10477746688999998778899999999998744499861777777752


No 215
>TIGR01172 cysE serine O-acetyltransferase; InterPro: IPR005881    The biosynthesis of L-cysteine is the predominant way by which inorganic sulphur is incorporated into organic compounds. In this process, the most abundant utilizable source of sulphur, inorganic sulphate, is taken up and reduced to sulphide. Sulphide is used to produce L-cysteine, which serves for protein synthesis or the production of other sulphur-containing organic compounds. Two routes for cysteine biosynthesis in nature have been documented. Serine transacetylase (2.3.1.30 from EC) catalyzes steps in pathway I, the activation of L-serine by acetyl-coenzyme A, yielding O-acetyl-L-serine.; GO: 0009001 serine O-acetyltransferase activity, 0006535 cysteine biosynthetic process from serine, 0005737 cytoplasm.
Probab=24.28  E-value=40  Score=12.71  Aligned_cols=14  Identities=29%  Similarity=0.458  Sum_probs=6.8

Q ss_pred             CCCEEEEEEECCCC
Q ss_conf             67236889623885
Q gi|254780879|r  443 DSELLYIHARFGET  456 (652)
Q Consensus       443 ~geil~A~~~~~g~  456 (652)
                      +.=.+|=..|++|.
T Consensus        92 ddv~iyhGVTLGGt  105 (163)
T TIGR01172        92 DDVTIYHGVTLGGT  105 (163)
T ss_pred             CCEEEEECEEECCC
T ss_conf             88378632120678


No 216
>PRK12839 hypothetical protein; Provisional
Probab=24.17  E-value=40  Score=12.69  Aligned_cols=24  Identities=8%  Similarity=-0.022  Sum_probs=16.1

Q ss_pred             CCHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             110256668871999899999999
Q gi|254780879|r  386 IYDGIWRATSFNGMNSNLVKLIMR  409 (652)
Q Consensus       386 I~~SLy~aa~~~gip~~ii~~lv~  409 (652)
                      ..+||-+.|.+.|++.....+-++
T Consensus       428 kadTleELA~~~gid~~~L~~TV~  451 (574)
T PRK12839        428 KGRTIEELAQKCGIDPAGLRATVT  451 (574)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             549999999886959899999999


No 217
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=24.17  E-value=40  Score=12.69  Aligned_cols=27  Identities=7%  Similarity=0.231  Sum_probs=16.7

Q ss_pred             CHHHCCCCCEEEEEECCCCCCCEEEEE
Q ss_conf             610169988899997278886405899
Q gi|254780879|r  313 RVDQLTKDEILRIGVVQKDDKFTIVRF  339 (652)
Q Consensus       313 ~~~~Lr~Gq~L~I~~~~~~~~~~~~r~  339 (652)
                      .+..|++|+++++.+.+.++...+..+
T Consensus        84 ~l~~lk~Gd~V~F~Fvq~G~~~~l~~I  110 (114)
T PRK09838         84 KMSEIKTGDKVAFNFVQQGNLSLLQDI  110 (114)
T ss_pred             HHHCCCCCCEEEEEEEEECCEEEEEEE
T ss_conf             760599999899999963997799998


No 218
>COG1820 NagA N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]
Probab=24.10  E-value=28  Score=13.75  Aligned_cols=11  Identities=18%  Similarity=0.102  Sum_probs=4.0

Q ss_pred             CEEEEEECCCC
Q ss_conf             01368841797
Q gi|254780879|r  275 ADDLIPIQHNT  285 (652)
Q Consensus       275 ~e~~v~VK~GD  285 (652)
                      .+.-|+|.-|-
T Consensus       183 ~~~giivs~GH  193 (380)
T COG1820         183 ANAGIVVSIGH  193 (380)
T ss_pred             HHCCEEEEECC
T ss_conf             86893997157


No 219
>PRK08291 ornithine cyclodeaminase; Validated
Probab=24.00  E-value=40  Score=12.67  Aligned_cols=15  Identities=7%  Similarity=0.020  Sum_probs=6.8

Q ss_pred             CCCCHHHCCCCCEEE
Q ss_conf             015610169988899
Q gi|254780879|r  310 NEVRVDQLTKDEILR  324 (652)
Q Consensus       310 ~~~~~~~Lr~Gq~L~  324 (652)
                      ..++...|++|..+.
T Consensus       210 Pv~~~~~lkpG~hI~  224 (330)
T PRK08291        210 PILKAEWLHPGLHVT  224 (330)
T ss_pred             CCCCHHHCCCCCEEE
T ss_conf             501510069982899


No 220
>PRK11308 dppF dipeptide transporter ATP-binding subunit; Provisional
Probab=23.85  E-value=40  Score=12.65  Aligned_cols=11  Identities=9%  Similarity=0.069  Sum_probs=8.0

Q ss_pred             CCEEEEEEEEE
Q ss_conf             54068875321
Q gi|254780879|r  424 TDFLETFFSVN  434 (652)
Q Consensus       424 GD~f~Vlye~~  434 (652)
                      .|+.-|+|...
T Consensus       222 aDri~VMy~G~  232 (327)
T PRK11308        222 ADDVMVMYLGR  232 (327)
T ss_pred             CCEEEEEECCE
T ss_conf             99899998988


No 221
>PRK09099 type III secretion system ATPase; Provisional
Probab=23.63  E-value=41  Score=12.62  Aligned_cols=26  Identities=12%  Similarity=0.038  Sum_probs=15.5

Q ss_pred             CCEEECCCCCCCEEECCCCEEEEEEE
Q ss_conf             20030267967279715967999653
Q gi|254780879|r  514 TGVDWAAPRGTPIVAVGDGIVEKANW  539 (652)
Q Consensus       514 ~GVD~aAp~GTPI~Aag~G~V~~ag~  539 (652)
                      .|=|+..|.-+-+++.-||-++-...
T Consensus       317 ~~dd~~~pi~d~~~si~DGhivLsr~  342 (441)
T PRK09099        317 EDDSGSDPIAEEVRGILDGHMILSRE  342 (441)
T ss_pred             CCCCCCCCHHHHHHHHCCEEEEECHH
T ss_conf             68877787678777670638998587


No 222
>TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit; InterPro: IPR008703 This family consists of several bacterial Na^+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na^+-translocating NADH: ubiquinone oxidoreductase (Na^+-NQR) generates an electrochemical Na^+ potential driven by aerobic respiration .; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006814 sodium ion transport.
Probab=23.53  E-value=25  Score=14.05  Aligned_cols=24  Identities=17%  Similarity=0.011  Sum_probs=15.1

Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             444556503344320233322245
Q gi|254780879|r  199 QLDHTAQDEEIKNAIMNQFFLLHN  222 (652)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~  222 (652)
                      ..-.+++.+.+...+-+.+.|..-
T Consensus       108 ~~L~~Ls~~~~~~~l~~sGLw~~~  131 (466)
T TIGR01936       108 YDLATLSAEQIKELLLESGLWTAL  131 (466)
T ss_pred             CCHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             460103789999998740057676


No 223
>COG4729 Uncharacterized conserved protein [Function unknown]
Probab=23.50  E-value=41  Score=12.61  Aligned_cols=40  Identities=23%  Similarity=0.346  Sum_probs=19.8

Q ss_pred             CCCEEECCCEEEEECCC-----CCCCCCEEEEEEEECCEECCCCE
Q ss_conf             99788349589984166-----78887426889978678836620
Q gi|254780879|r  571 AGTAVKQGQIIGWIGTT-----GLSTGPHLHYELIVNGIKVDSTK  610 (652)
Q Consensus       571 ~G~~V~qGQvIG~vGsT-----G~STGPHLHfEv~vnG~~VdP~~  610 (652)
                      +|..+.-||.++|-+.-     -+|++|--||.+-+||+.++-.+
T Consensus        87 ~~~t~~dg~~~~y~~~~~~~~L~~~~s~~~~~~l~vngr~~~l~~  131 (156)
T COG4729          87 EGATLEDGAWFYYRGVRTLQVLRWSRSREAGYRLCVNGRSYALAR  131 (156)
T ss_pred             CCEEEECCCEEEECCCCCEEEEEEECCCCCCEEEEECCEEEEEEC
T ss_conf             855874797798736763346898616645278860887887323


No 224
>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional
Probab=23.37  E-value=41  Score=12.59  Aligned_cols=19  Identities=11%  Similarity=0.347  Sum_probs=8.4

Q ss_pred             HHHHCCCCHHHHHHHHHHH
Q ss_conf             9997499989999999985
Q gi|254780879|r  290 AMVHAGYSNGDSAKIAKAL  308 (652)
Q Consensus       290 IL~r~Gvs~~ei~~i~~al  308 (652)
                      .+.-.|++..++.+.+..+
T Consensus       109 ~~~~~g~~~~~~~~~~~~~  127 (264)
T PRK13546        109 KMLCMGFKRKEIKAMTPKI  127 (264)
T ss_pred             HHHHCCCCHHHHHHHHHHH
T ss_conf             9987242499999999999


No 225
>TIGR00396 leuS_bact leucyl-tRNA synthetase; InterPro: IPR002302   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .    Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes the eubacterial and mitochondrial synthetases. The crystal structure of leucyl-tRNA synthetase from the hyperthermophile Thermus thermophilus has an overall architecture that is similar to that of isoleucyl-tRNA synthetase, except that the putative editing domain is inserted at a different position in the primary structure. This feature is unique to prokaryote-like leucyl-tRNA synthetases, as is the presence of a novel additional flexibly inserted domain . ; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=23.29  E-value=37  Score=12.95  Aligned_cols=244  Identities=14%  Similarity=0.127  Sum_probs=105.0

Q ss_pred             CCCCEEEEEECCCCCHHHHHHH-----CCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEE-ECCCCCCCEEEEEEECCCC
Q ss_conf             7640136884179708999997-----499989999999985401561016998889999-7278886405899971688
Q gi|254780879|r  272 PEFADDLIPIQHNTTIFDAMVH-----AGYSNGDSAKIAKALKNEVRVDQLTKDEILRIG-VVQKDDKFTIVRFSIYHKQ  345 (652)
Q Consensus       272 ~~~~e~~v~VK~GDTL~~IL~r-----~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~-~~~~~~~~~~~r~si~~~~  345 (652)
                      ..+.++.+.+.+-.+...+|.+     .|+...++.+.+...-...+..+-+.-=+||=. +++.       |+   =|.
T Consensus       390 ~A~t~~g~~~ns~tstdGvltkeC~~f~Gl~~~~A~~~I~~~L~~~~~gk~~v~YrLRDW~~SRQ-------RY---WG~  459 (916)
T TIGR00396       390 QAYTEDGVLVNSSTSTDGVLTKECGEFNGLNSSEAKEAIIKMLEKEGKGKRKVNYRLRDWLFSRQ-------RY---WGE  459 (916)
T ss_pred             HHHHHCCCEECCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEECCCEEEE-------CC---CCC
T ss_conf             76764652216876534410100022237761789999999998638850212346532534400-------02---688


Q ss_pred             CEEEEEEECCCCCEEECCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHCCCCC
Q ss_conf             34899984278843201333210000012211123345421102566688719998999999997301110121014454
Q gi|254780879|r  346 KHLLTIALNDNNEYVLGVEPVKMDINHQMDYMRTSEESPNIYDGIWRATSFNGMNSNLVKLIMRTLASSVNLQEHLKPTD  425 (652)
Q Consensus       346 ~~~~~va~~d~g~fv~~~ep~~~~~~~~~~~~~~~~~~~~I~~SLy~aa~~~gip~~ii~~lv~i~a~dVDFqr~ir~GD  425 (652)
                      ..-  +--.+.|..++..+   -.....-++.......|++.+           |-.-+.+-+++-.-...+. ..|..|
T Consensus       460 PIP--iih~e~g~~~P~~~---~dLPv~LP~~~~~~~~G~~~s-----------PL~~~~~W~~v~~~~~~~~-A~RETd  522 (916)
T TIGR00396       460 PIP--IIHCEDGGAVPVPE---EDLPVKLPELVNYDGSGTGES-----------PLSRIKEWVNVTCPSCGKP-ALRETD  522 (916)
T ss_pred             CCC--EEEECCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCC-----------HHHHCCCCEEECCCCCCCC-CCCCCC
T ss_conf             987--78806768424434---468710750023578889888-----------0430746324147887987-543378


Q ss_pred             EEEEEEE---------EEC-CC-----CCCCCC---CCEEEEEEECCCCCCC-----CCCCCCCCCCCCCCCCCCCCCH-
Q ss_conf             0688753---------211-57-----851246---7236889623885420-----1345576655444335566100-
Q gi|254780879|r  426 FLETFFS---------VNH-AN-----NQASDD---SELLYIHARFGETRTR-----FYRFLNPVDGSVEYFNENGKSS-  481 (652)
Q Consensus       426 ~f~Vlye---------~~~-~~-----g~~~~~---geil~A~~~~~g~~~~-----~yrf~~~~~~~~~yyd~~G~S~-  481 (652)
                      ++.-+.+         ..- ..     .+..+.   ..=|.+.++.||-++-     |.||-++--.     |..--+. 
T Consensus       523 TMdtf~~SsWYylRY~~p~~n~~FWPi~~~~d~e~~~~wlPVD~YiGG~EHAiLHLLY~RF~hK~L~-----D~g~v~~P  597 (916)
T TIGR00396       523 TMDTFIGSSWYYLRYLDPKNNTNFWPIDQPFDKEKAEYWLPVDLYIGGIEHAILHLLYARFFHKFLY-----DLGLVSTP  597 (916)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHH-----HCCCCCCC
T ss_conf             7630577789998603500176668732130278897558844102626899899888899999997-----45761587


Q ss_pred             --HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCCEEEEEEEECCCCCEEEEECCCC-EEEE
Q ss_conf             --0001123334541023567641434044346420030267967279715967999653089700799983997-4882
Q gi|254780879|r  482 --RPFLLRTPVPFGRMTSGFGMRYHPILGYSRMHTGVDWAAPRGTPIVAVGDGIVEKANWAGGYGKQTLIHHGNG-YVSS  558 (652)
Q Consensus       482 --~k~llr~Pv~~~risS~Fg~R~hPilg~~r~H~GVD~aAp~GTPI~Aag~G~V~~ag~~~GyGn~V~I~H~~G-y~T~  558 (652)
                        -+-.+.+-+.-|-|.+                +|.-|..|.|--+.-.=.-.|+. +.+.+-++-+.+..++. ..+.
T Consensus       598 aGi~EPFkKL~~QGMVlg----------------~~f~y~~~~g~~~W~~p~d~~~~-~d~~~d~~~~~d~~~~~~~~~~  660 (916)
T TIGR00396       598 AGIKEPFKKLINQGMVLG----------------DAFYYKKPNGKRIWVVPADELIE-RDEKGDIKKAKDKSGGELVVVG  660 (916)
T ss_pred             CCCCCHHHHHHHCCEEEC----------------CCEEECCCCCCEEEEECCCCEEE-CCCCCCCCCCEECCCCCEEEEE
T ss_conf             766571455420000211----------------61341389973677645751661-0466786542325888247887


Q ss_pred             EHHHHH
Q ss_conf             002144
Q gi|254780879|r  559 YNHQDA  564 (652)
Q Consensus       559 YaHlS~  564 (652)
                      |+=||+
T Consensus       661 ~~KMSK  666 (916)
T TIGR00396       661 YEKMSK  666 (916)
T ss_pred             EEEECC
T ss_conf             776202


No 226
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit; InterPro: IPR005683    The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins.The inner membrane translocase is formed of a complex with a number of proteins, including the Tim17, Tim23 and Tim44 subunits. This family is specific for the Tom22 proteins. ; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane.
Probab=23.26  E-value=39  Score=12.75  Aligned_cols=25  Identities=24%  Similarity=0.328  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             9999999999876268841004862
Q gi|254780879|r   52 TSGVIIGGSLLTALDGHQKIAIPAK   76 (652)
Q Consensus        52 ~~~~l~g~a~~~aldg~~~~a~p~~   76 (652)
                      |+++|||+=+..||..+++++.-++
T Consensus       104 tsaLLlGVPf~~s~~eeq~l~emEk  128 (152)
T TIGR00986       104 TSALLLGVPFALSLAEEQQLIEMEK  128 (152)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9899988899999998768999988


No 227
>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]
Probab=23.18  E-value=41  Score=12.57  Aligned_cols=19  Identities=26%  Similarity=0.665  Sum_probs=14.8

Q ss_pred             CCCEEECCCEEEEECCCCC
Q ss_conf             9978834958998416678
Q gi|254780879|r  571 AGTAVKQGQIIGWIGTTGL  589 (652)
Q Consensus       571 ~G~~V~qGQvIG~vGsTG~  589 (652)
                      ..-..++||.+|.||-+|.
T Consensus       306 isl~L~~gqTlGlVGESGS  324 (534)
T COG4172         306 ISLTLRRGQTLGLVGESGS  324 (534)
T ss_pred             CEEEECCCCEEEEEECCCC
T ss_conf             4367538976777705889


No 228
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=23.13  E-value=42  Score=12.56  Aligned_cols=45  Identities=16%  Similarity=0.217  Sum_probs=26.3

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCEEEEEHHHHHHHHC--CCCCCEEECCCEE
Q ss_conf             96799965308970079998399748820021445411--8899788349589
Q gi|254780879|r  531 DGIVEKANWAGGYGKQTLIHHGNGYVSSYNHQDAIAKN--IKAGTAVKQGQII  581 (652)
Q Consensus       531 ~G~V~~ag~~~GyGn~V~I~H~~Gy~T~YaHlS~~a~g--V~~G~~V~qGQvI  581 (652)
                      .|+|...-   .||-+|.+.   +..+.+.|.|.+...  ..+-..++.||.|
T Consensus         2 ~G~V~~i~---~~G~fV~~~---~~~~gli~~s~~s~~~~~~~~~~~~~G~~V   48 (65)
T cd00164           2 TGKVVSIT---KFGVFVELE---DGVEGLVHISELSDKFVKDPSEVFKVGDEV   48 (65)
T ss_pred             EEEEEEEE---CCEEEEEEC---CCEEEEEEHHHHCCCCCCCHHHEECCCCEE
T ss_conf             89999997---845999989---871788988891676535951098599999


No 229
>pfam04239 DUF421 Protein of unknown function (DUF421). YDFR family
Probab=23.05  E-value=42  Score=12.55  Aligned_cols=40  Identities=8%  Similarity=0.155  Sum_probs=31.7

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCC
Q ss_conf             68841797089999974999899999999854015610169
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLT  318 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr  318 (652)
                      ++.|+.|.-+...+++.+++.+|+...+.. ++.+++..++
T Consensus         9 ~~li~~G~i~~~~l~k~~it~~dl~~~LR~-~gi~~~~~V~   48 (98)
T pfam04239         9 TLLIENGKILEENLKKERLTEDDLLSALRE-KGIFDLSDVE   48 (98)
T ss_pred             EEEEECCEECHHHHHHCCCCHHHHHHHHHH-CCCCCHHHHC
T ss_conf             799999999699998849999999999998-3999988902


No 230
>TIGR02465 chlorocat_1_2 chlorocatechol 1,2-dioxygenase; InterPro: IPR012817    Members of this protein family are chlorocatechol 1,2-dioxygenase. This protein is closely related to catechol 1,2-dioxygenase, IPR012801 from INTERPRO, 1.13.11.1 from EC. Note: a number of annotated database entries for members of this family have EC numbers that refers to IPR012801 from INTERPRO; whereas members of this family acts in pathways for the biodegradation of chlorinated aromatic compounds.; GO: 0005506 iron ion binding, 0018575 chlorocatechol 12-dioxygenase activity, 0006725 aromatic compound metabolic process.
Probab=23.03  E-value=40  Score=12.67  Aligned_cols=26  Identities=12%  Similarity=0.106  Sum_probs=14.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             89999974999899999999854015
Q gi|254780879|r  287 IFDAMVHAGYSNGDSAKIAKALKNEV  312 (652)
Q Consensus       287 L~~IL~r~Gvs~~ei~~i~~al~~~~  312 (652)
                      +-++|.+.-|+.+|=..++.-|-+..
T Consensus        15 vR~~L~~heVT~~EYr~g~~Yl~~v~   40 (258)
T TIGR02465        15 VRDVLVRHEVTEDEYRTGVQYLMKVA   40 (258)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             99987406688478999999988643


No 231
>pfam08724 Rep_N Rep protein catalytic domain like. Adeno-associated virus (AAV) Replication (Rep) protein is essential for viral replication and integration. The catalytic domain has DNA binding and endonuclease activity.
Probab=22.94  E-value=42  Score=12.54  Aligned_cols=11  Identities=9%  Similarity=0.075  Sum_probs=4.7

Q ss_pred             EEEEECCCCCH
Q ss_conf             36884179708
Q gi|254780879|r  277 DLIPIQHNTTI  287 (652)
Q Consensus       277 ~~v~VK~GDTL  287 (652)
                      -+|++-.|..+
T Consensus        86 HlHvlI~~~gv   96 (186)
T pfam08724        86 HLHVLIGGPGV   96 (186)
T ss_pred             EEEEEECCCCC
T ss_conf             79999648997


No 232
>PRK03695 vitamin B12-transporter ATPase; Provisional
Probab=22.54  E-value=43  Score=12.48  Aligned_cols=22  Identities=5%  Similarity=0.030  Sum_probs=8.9

Q ss_pred             ECCCCCCCEEECCCCEEEEEEE
Q ss_conf             0267967279715967999653
Q gi|254780879|r  518 WAAPRGTPIVAVGDGIVEKANW  539 (652)
Q Consensus       518 ~aAp~GTPI~Aag~G~V~~ag~  539 (652)
                      ++...-.-|+--.+|.|+..|-
T Consensus       192 ~~~~~~dri~vl~~G~iv~~G~  213 (245)
T PRK03695        192 HTLRHADRVWLLKQGKLLASGR  213 (245)
T ss_pred             HHHHHCCEEEEEECCEEEEEEC
T ss_conf             9999799999998998999907


No 233
>pfam08986 DUF1889 Domain of unknown function (DUF1889). This domain is found in a set of hypothetical bacterial proteins.
Probab=22.29  E-value=13  Score=16.07  Aligned_cols=17  Identities=29%  Similarity=0.634  Sum_probs=6.8

Q ss_pred             CCEEEEECCCCEEEEEHH
Q ss_conf             007999839974882002
Q gi|254780879|r  544 GKQTLIHHGNGYVSSYNH  561 (652)
Q Consensus       544 Gn~V~I~H~~Gy~T~YaH  561 (652)
                      |+.|+|+|. .|-+.|.|
T Consensus        96 GerivIKnP-EyFstYM~  112 (119)
T pfam08986        96 GERIVIKNP-EYFSTYMQ  112 (119)
T ss_pred             CCEEEECCH-HHHHHHHH
T ss_conf             774775495-89999999


No 234
>TIGR02441 fa_ox_alpha_mit fatty acid oxidation complex, alpha subunit, mitochondrial; InterPro: IPR012803    Members of this family represent the alpha subunit of the mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (4.2.1.17 from EC) and 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC). Some characterization of these proteins has been done in human (P40939 from SWISSPROT), pig (Q29554 from SWISSPROT) and rat (Q64428 from SWISSPROT). The beta subunit has acetyl-CoA C-acyltransferase (2.3.1.16 from EC) activity.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0004300 enoyl-CoA hydratase activity, 0006635 fatty acid beta-oxidation, 0005739 mitochondrion, 0016507 fatty acid beta-oxidation multienzyme complex.
Probab=22.27  E-value=43  Score=12.44  Aligned_cols=34  Identities=26%  Similarity=0.427  Sum_probs=18.0

Q ss_pred             CCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             35566100000112333454102356764143404
Q gi|254780879|r  474 FNENGKSSRPFLLRTPVPFGRMTSGFGMRYHPILG  508 (652)
Q Consensus       474 yd~~G~S~~k~llr~Pv~~~risS~Fg~R~hPilg  508 (652)
                      -+|----+.-..|-.|..+ -|.|-||.-.=|.+|
T Consensus       659 vNEA~lCL~EgiL~~P~eG-DigaVFGlGFPPf~G  692 (740)
T TIGR02441       659 VNEAVLCLEEGILASPLEG-DIGAVFGLGFPPFLG  692 (740)
T ss_pred             HHHHHHHHHCCCCCCCCCC-CEEEECCCCCCCCCC
T ss_conf             8999986303423778887-616662667888885


No 235
>TIGR02645 ARCH_P_rylase putative thymidine phosphorylase; InterPro: IPR013466    Proteins in this entry are closely related to characterised examples of thymidine phosphorylase (2.4.2.4 from EC) and pyrimidine nucleoside phosphorylase (2.4.2.2 from EC). Most examples are found in the archaea, but other examples are found in bacteria such as Legionella pneumophila (strain Paris) and Rhodopseudomonas palustris CGA009.; GO: 0009032 thymidine phosphorylase activity.
Probab=22.19  E-value=34  Score=13.20  Aligned_cols=24  Identities=8%  Similarity=0.178  Sum_probs=20.1

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             999974999899999999854015
Q gi|254780879|r  289 DAMVHAGYSNGDSAKIAKALKNEV  312 (652)
Q Consensus       289 ~IL~r~Gvs~~ei~~i~~al~~~~  312 (652)
                      .+|.|-.++.+|+.+|++..++-.
T Consensus       212 EVLtrV~ls~~E~K~iV~~~ggcL  235 (499)
T TIGR02645       212 EVLTRVELSVEEIKRIVEKVGGCL  235 (499)
T ss_pred             EEECCCCCCHHHHHHHHHHCCCEE
T ss_conf             672165224788989986408645


No 236
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=22.06  E-value=35  Score=13.10  Aligned_cols=32  Identities=6%  Similarity=0.043  Sum_probs=21.4

Q ss_pred             EECCCEEEEECCCCCCCCCCCCCCCCHHHHHC
Q ss_conf             64571002100236553335897987125522
Q gi|254780879|r  130 KKIPFAYARMTFATPYPKVKDHPKFDPLKIFS  161 (652)
Q Consensus       130 ~~~pf~~~~~~l~~~~~~~~~~p~f~p~~~~~  161 (652)
                      -.-|.+.|+.+-.-..+.+..||||||.-+..
T Consensus       132 p~iP~iLvNGa~GIgtG~sT~IP~hNp~eii~  163 (445)
T cd00187         132 PIFPNLLVNGSSGIAVGMATNIPPHNLREVID  163 (445)
T ss_pred             CCCHHHHHCCCEEEEEEECCCCCCCCHHHHHH
T ss_conf             43307763466133420005678878899999


No 237
>PRK04722 consensus
Probab=22.05  E-value=44  Score=12.41  Aligned_cols=33  Identities=6%  Similarity=0.007  Sum_probs=20.1

Q ss_pred             HHHHHCCCCHHHHHH----HHHHHHCCCCHHHCCCCCE
Q ss_conf             999974999899999----9998540156101699888
Q gi|254780879|r  289 DAMVHAGYSNGDSAK----IAKALKNEVRVDQLTKDEI  322 (652)
Q Consensus       289 ~IL~r~Gvs~~ei~~----i~~al~~~~~~~~Lr~Gq~  322 (652)
                      .-.+.|+++-+|+..    --.+++..+ .++|++|-+
T Consensus        38 ~f~~~y~idm~Ea~~~~~~~Y~sfn~FF-tR~Lk~~~R   74 (280)
T PRK04722         38 TVTRKFGVDLSEAQEPDPRAYPTFNAFF-TRALKPGAR   74 (280)
T ss_pred             HHHHHHCCCHHHHCCCCHHHCCCHHHHE-EECCCCCCC
T ss_conf             9999979797897378823378788846-220577888


No 238
>PRK03598 hypothetical protein; Provisional
Probab=21.78  E-value=44  Score=12.38  Aligned_cols=14  Identities=7%  Similarity=0.145  Sum_probs=7.7

Q ss_pred             HHCCCCCEEEEEEE
Q ss_conf             10144540688753
Q gi|254780879|r  419 EHLKPTDFLETFFS  432 (652)
Q Consensus       419 r~ir~GD~f~Vlye  432 (652)
                      ..+++|+..+|...
T Consensus       252 ~~v~~Gq~v~i~~d  265 (331)
T PRK03598        252 GQAQPGRKVLVYTD  265 (331)
T ss_pred             HHCCCCCEEEEEEE
T ss_conf             52889998999994


No 239
>cd03795 GT1_like_4 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP-linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=21.41  E-value=38  Score=12.81  Aligned_cols=29  Identities=24%  Similarity=0.226  Sum_probs=15.6

Q ss_pred             CCCCCCCEEECCCC-EEEEEEEECCCCCEE
Q ss_conf             26796727971596-799965308970079
Q gi|254780879|r  519 AAPRGTPIVAVGDG-IVEKANWAGGYGKQT  547 (652)
Q Consensus       519 aAp~GTPI~Aag~G-~V~~ag~~~GyGn~V  547 (652)
                      |..+|+||+|+.-| -....-.++..|.++
T Consensus       285 Ama~G~PVVat~~gg~~~~i~~~~~~G~l~  314 (357)
T cd03795         285 AMAFGKPVISTEIGTGGSYVNLHGVTGLVV  314 (357)
T ss_pred             HHHCCCCEEEECCCCCHHHHEECCCEEEEE
T ss_conf             998799899935999815605569579997


No 240
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=21.23  E-value=45  Score=12.30  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=17.4

Q ss_pred             CCEEECCCEEEEECCCCCCCCCEE
Q ss_conf             978834958998416678887426
Q gi|254780879|r  572 GTAVKQGQIIGWIGTTGLSTGPHL  595 (652)
Q Consensus       572 G~~V~qGQvIG~vGsTG~STGPHL  595 (652)
                      =+....|+|||.+|.-...||--|
T Consensus        59 ie~A~aGDIvav~g~~~~~tGDTL   82 (85)
T cd03689          59 VDEAYPGDIIGLVNPGNFQIGDTL   82 (85)
T ss_pred             ECEEECCCEEEEECCCCCEECCCC
T ss_conf             034938989998279987314651


No 241
>pfam05775 AfaD Enterobacteria AfaD invasin protein. This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells.
Probab=21.22  E-value=45  Score=12.30  Aligned_cols=10  Identities=30%  Similarity=0.219  Sum_probs=5.1

Q ss_pred             HHCCCCCEEE
Q ss_conf             0169988899
Q gi|254780879|r  315 DQLTKDEILR  324 (652)
Q Consensus       315 ~~Lr~Gq~L~  324 (652)
                      ..|+.|++|-
T Consensus        31 ~~lrDG~~ia   40 (136)
T pfam05775        31 GQLRDGMKLA   40 (136)
T ss_pred             CCCCCCCEEE
T ss_conf             4234773887


No 242
>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=21.21  E-value=45  Score=12.30  Aligned_cols=14  Identities=7%  Similarity=0.166  Sum_probs=6.6

Q ss_pred             HHHCCCCHHHHHHH
Q ss_conf             99749998999999
Q gi|254780879|r  291 MVHAGYSNGDSAKI  304 (652)
Q Consensus       291 L~r~Gvs~~ei~~i  304 (652)
                      ++..|++.+++.+.
T Consensus       107 l~~~g~~~~e~~~r  120 (279)
T PRK13635        107 LENIGVPREEMVER  120 (279)
T ss_pred             HHHCCCCHHHHHHH
T ss_conf             98779999999999


No 243
>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional
Probab=21.18  E-value=45  Score=12.30  Aligned_cols=15  Identities=47%  Similarity=1.077  Sum_probs=7.6

Q ss_pred             EEECCCEEEEECCCC
Q ss_conf             883495899841667
Q gi|254780879|r  574 AVKQGQIIGWIGTTG  588 (652)
Q Consensus       574 ~V~qGQvIG~vGsTG  588 (652)
                      .|++|+++|.+|-.|
T Consensus       275 ~v~~GEivgivG~nG  289 (501)
T PRK11288        275 AVRRGEIVGFFGLVG  289 (501)
T ss_pred             EEECCEEEEEECCCC
T ss_conf             870883999756888


No 244
>PRK13633 cobalt transporter ATP-binding subunit; Provisional
Probab=21.13  E-value=45  Score=12.29  Aligned_cols=25  Identities=8%  Similarity=0.033  Sum_probs=12.2

Q ss_pred             HHHHCCCCHHHHHHHHHHHHCCCCH
Q ss_conf             9997499989999999985401561
Q gi|254780879|r  290 AMVHAGYSNGDSAKIAKALKNEVRV  314 (652)
Q Consensus       290 IL~r~Gvs~~ei~~i~~al~~~~~~  314 (652)
                      -++..|++.+++.+-+...-....+
T Consensus       111 g~~~~g~~~~e~~~rv~~~l~~~gL  135 (281)
T PRK13633        111 GPENLGIPPEEIRERVDESLKKVGM  135 (281)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHCCC
T ss_conf             8988699999999999999986794


No 245
>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules.  Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells.  Subsequently, virus-infected or malignantly transformed cells can be eliminated.  TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
Probab=21.08  E-value=45  Score=12.28  Aligned_cols=29  Identities=7%  Similarity=0.060  Sum_probs=11.9

Q ss_pred             CCEEEEEECCCCCHHHHHHHCCCCHHHHHH
Q ss_conf             401368841797089999974999899999
Q gi|254780879|r  274 FADDLIPIQHNTTIFDAMVHAGYSNGDSAK  303 (652)
Q Consensus       274 ~~e~~v~VK~GDTL~~IL~r~Gvs~~ei~~  303 (652)
                      ...-...|++|+.+. |.-..|--...+.+
T Consensus        30 L~~is~~i~~Ge~va-IvG~sGsGKSTL~~   58 (226)
T cd03248          30 LQDVSFTLHPGEVTA-LVGPSGSGKSTVVA   58 (226)
T ss_pred             EECEEEEECCCCEEE-EECCCCCHHHHHHH
T ss_conf             745389982999999-99999984999999


No 246
>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE).  The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE).  The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis.  The molecular mechanism of nickel uptake in many bacteria and most archaea is not known.  Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides.  The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.
Probab=21.01  E-value=46  Score=12.27  Aligned_cols=25  Identities=16%  Similarity=0.272  Sum_probs=12.1

Q ss_pred             EEECCCCCHHHHHHHCCCCHHHHHHH
Q ss_conf             88417970899999749998999999
Q gi|254780879|r  279 IPIQHNTTIFDAMVHAGYSNGDSAKI  304 (652)
Q Consensus       279 v~VK~GDTL~~IL~r~Gvs~~ei~~i  304 (652)
                      ..|++|+.+ .|+-..|.-.....++
T Consensus        26 l~i~~Ge~~-~iiG~sGsGKSTLl~~   50 (228)
T cd03257          26 FSIKKGETL-GLVGESGSGKSTLARA   50 (228)
T ss_pred             EEECCCCEE-EEECCCCCHHHHHHHH
T ss_conf             898699899-9999999869999999


No 247
>TIGR00848 fruA PTS system, fructose subfamily, IIA component; InterPro: IPR004715   The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) ,  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.   The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).    The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.    An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , .    The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.     The PTS Fructose-Mannitol (Fru) family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several putative PTS permeases of unknown specificities. The fructose permeases of this family phosphorylate fructose on the 1-position. Those of family 4.6 phosphorylate fructose on the 6-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family.    This family is specific for the IIA domain of the fructose PTS transporters. Also similar to the Enzyme IIA Fru subunits of the PTS is Enzyme IIA Ntr (nitrogen) found in Escherichia coli and other organisms, which may play a solely regulatory role.  ; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane.
Probab=20.88  E-value=38  Score=12.84  Aligned_cols=43  Identities=9%  Similarity=0.135  Sum_probs=18.1

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCCCCEEEEEECC
Q ss_conf             08999997499989999999985401561016998889999727
Q gi|254780879|r  286 TIFDAMVHAGYSNGDSAKIAKALKNEVRVDQLTKDEILRIGVVQ  329 (652)
Q Consensus       286 TL~~IL~r~Gvs~~ei~~i~~al~~~~~~~~Lr~Gq~L~I~~~~  329 (652)
                      .|+..|...|+-.+ ..+..+.+..+=....--.|+-+-|+-.+
T Consensus        23 ~La~~l~~~G~~~d-~~~f~~~~~~RE~~~~TG~g~gvAiPH~k   65 (133)
T TIGR00848        23 FLANKLLENGYISD-KEEFLEDLLKREEEGTTGIGDGVAIPHAK   65 (133)
T ss_pred             HHHHHHHHCCCCCC-HHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             99999984465378-89999999988630588664441045332


No 248
>COG3767 Uncharacterized low-complexity protein [Function unknown]
Probab=20.63  E-value=46  Score=12.22  Aligned_cols=30  Identities=17%  Similarity=0.310  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHH-HHCCCCCCCCCC
Q ss_conf             899999999999999987-626884100486
Q gi|254780879|r   46 TFFAGITSGVIIGGSLLT-ALDGHQKIAIPA   75 (652)
Q Consensus        46 t~ltg~~~~~l~g~a~~~-aldg~~~~a~p~   75 (652)
                      .+++-++|++|||.+.-+ ++.+...|++-+
T Consensus         5 ~~~~alagA~~l~~a~~~~a~~~~~~fav~~   35 (95)
T COG3767           5 ATAAALAGALLLGAAAVAQAENKSASFAVGA   35 (95)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             8899998789999888889872678553333


No 249
>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=20.62  E-value=46  Score=12.22  Aligned_cols=10  Identities=10%  Similarity=0.116  Sum_probs=3.6

Q ss_pred             CCCCHHHHHH
Q ss_conf             4999899999
Q gi|254780879|r  294 AGYSNGDSAK  303 (652)
Q Consensus       294 ~Gvs~~ei~~  303 (652)
                      .|++.+++.+
T Consensus       111 ~g~~~~e~~~  120 (285)
T PRK13636        111 LKLPEDEVRK  120 (285)
T ss_pred             CCCCHHHHHH
T ss_conf             5999999999


No 250
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase; InterPro: IPR004393   Nicotinate-nucleotide pyrophosphorylase (2.4.2.19 from EC), also known as quinolinate phosphoribosyltransferase (decarboxylating), catalyses the conversion of nicotinate D-ribonucleotide, pyrophosphate and carbon dioxide into pyridine-2,3-dicarboxylate and 5-phospho-alpha-D-ribose 1-diphosphate. This enzyme is a type II phosphoribosyltransferase which provides the de novo source of nicotinate mononucleotide (NAMN) for NAD biosynthesis in both prokaryotes and eukaryotes , .   Structural studies have shown that the active form of this enzyme is a homodimer with an unsual fold , , . The N-terminal forms a mixed alpha/beta domain, while the C-terminal region forms a multi-stranded, open alpha/beta barrel. The active site is found at the C-terminal ends of the beta strands of the alpha/beta barrel, and is bordered by the N-terminal domain of the second subunit of the dimer. It contains several conserved charged residues thought to be important determinants of substrate binding and catalysis. ; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0019363 pyridine nucleotide biosynthetic process.
Probab=20.62  E-value=46  Score=12.22  Aligned_cols=13  Identities=23%  Similarity=0.327  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             9999999985401
Q gi|254780879|r  299 GDSAKIAKALKNE  311 (652)
Q Consensus       299 ~ei~~i~~al~~~  311 (652)
                      ...+++++++++.
T Consensus       107 T~Tr~~v~~~~~~  119 (276)
T TIGR00078       107 TATRKYVEALRGT  119 (276)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             9999999998458


No 251
>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=20.24  E-value=47  Score=12.16  Aligned_cols=15  Identities=20%  Similarity=0.237  Sum_probs=7.7

Q ss_pred             HHHCCCCHHHHHHHH
Q ss_conf             997499989999999
Q gi|254780879|r  291 MVHAGYSNGDSAKIA  305 (652)
Q Consensus       291 L~r~Gvs~~ei~~i~  305 (652)
                      ++..|++.+++.+.+
T Consensus       107 ~~~~~~~~~e~~~~v  121 (277)
T PRK13642        107 MENQGIPREEMIKRV  121 (277)
T ss_pred             HHHCCCCHHHHHHHH
T ss_conf             766699999999999


No 252
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=20.16  E-value=47  Score=12.15  Aligned_cols=24  Identities=8%  Similarity=0.066  Sum_probs=16.1

Q ss_pred             CCHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             110256668871999899999999
Q gi|254780879|r  386 IYDGIWRATSFNGMNSNLVKLIMR  409 (652)
Q Consensus       386 I~~SLy~aa~~~gip~~ii~~lv~  409 (652)
                      ..++|-+.|.+.|+|.....+-+.
T Consensus       376 ~adTleeLA~~~gi~~~~L~~Tv~  399 (515)
T PRK12837        376 TADTLEELAAKIGVPADALTATVA  399 (515)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             459899999986959999999999


No 253
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=20.08  E-value=24  Score=14.20  Aligned_cols=46  Identities=9%  Similarity=0.190  Sum_probs=30.3

Q ss_pred             EEEECCCCCHHHHHHHCCCCHHHHHHHHHHH------HCCCCHHHCCCCCEEEEE
Q ss_conf             6884179708999997499989999999985------401561016998889999
Q gi|254780879|r  278 LIPIQHNTTIFDAMVHAGYSNGDSAKIAKAL------KNEVRVDQLTKDEILRIG  326 (652)
Q Consensus       278 ~v~VK~GDTL~~IL~r~Gvs~~ei~~i~~al------~~~~~~~~Lr~Gq~L~I~  326 (652)
                      ...+..+-||.++|...++...-++   -++      +..+....|+.|+++.|.
T Consensus         9 ~~~~~~~~tl~~Ll~~l~~~~~~vA---VevN~~ivpr~~~~~~~L~egD~iEIv   60 (66)
T PRK05659          9 PRELPDGESVAALLAREGLAGRRVA---VEVNGEIVPRSQHASTALREGDVVEIV   60 (66)
T ss_pred             EEECCCCCCHHHHHHHCCCCCCCEE---EEECCEECCHHHHCCCCCCCCCEEEEE
T ss_conf             8786999969999987699998099---998998817789572658999999999


Done!